From tony.travis at abdn.ac.uk Wed Feb 12 10:32:59 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Wed, 12 Feb 2014 15:32:59 +0000 Subject: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: References: <1392144869.5335.3.camel@balisaur> Message-ID: <52FB942B.8070103@abdn.ac.uk> On 12/02/14 15:03, Jasmine Lognnes wrote: > Dear Tim, > > That's a very impressive script. Wow! > > By going through the script I have cherry picked what looks like to be > needed on a plain Ubuntu 12.04 64bit. I have attached it as a script. > Can you verify that it is the correct procedure? > > On the liveUSB I did > > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}' > > and got the attached list of packages. On a successful installation, > should I end up these exact packages? Hi, Jasmine. I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu 12.04 LTS systems without any problems. You don't need to grep things out like you did. Just run the script in its entirety and please email any bug reports to the bio-linux-dev list. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. From princess.jasmine.lognnes at gmail.com Thu Feb 13 10:06:54 2014 From: princess.jasmine.lognnes at gmail.com (Jasmine Lognnes) Date: Thu, 13 Feb 2014 16:06:54 +0100 Subject: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: <52FB942B.8070103@abdn.ac.uk> References: <1392144869.5335.3.camel@balisaur> <52FB942B.8070103@abdn.ac.uk> Message-ID: Dear Tony, That is good news. I have now tried it on a fresh Ubuntu 12.04 64bit, and it exits with pasted in at the bottom. More complete output attached. What can you gather from this? Hugs, Jasmine =) The following NEW packages will be installed: bio-linux-artemis 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded. Need to get 11.8 MB of archives. After this operation, 47.7 MB of additional disk space will be used. Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-artemis all 15.1.1-1 [11.8 MB] Fetched 11.8 MB in 2s (5,111 kB/s) Selecting previously unselected package bio-linux-artemis. (Reading database ... 162928 files and directories currently installed.) Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.deb) ... Processing triggers for bamfdaemon ... Rebuilding /usr/share/applications/bamf.index... Processing triggers for desktop-file-utils ... Processing triggers for gnome-menus ... Setting up bio-linux-artemis (15.1.1-1) ... Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package bio-linux-assembly-conversion-tools Not all packages installed properly - exiting. On 12 February 2014 16:32, Tony Travis wrote: > On 12/02/14 15:03, Jasmine Lognnes wrote: > > Dear Tim, > > > > That's a very impressive script. Wow! > > > > By going through the script I have cherry picked what looks like to be > > needed on a plain Ubuntu 12.04 64bit. I have attached it as a script. > > Can you verify that it is the correct procedure? > > > > On the liveUSB I did > > > > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}' > > > > and got the attached list of packages. On a successful installation, > > should I end up these exact packages? > > Hi, Jasmine. > > I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu > 12.04 LTS systems without any problems. You don't need to grep things > out like you did. Just run the script in its entirety and please email > any bug reports to the bio-linux-dev list. > > HTH, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > The University of Aberdeen is a charity registered in Scotland, No > SC013683. > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- Setting up libsub-name-perl (0.05-1build2) ... Setting up libtask-weaken-perl (1.03-1) ... Setting up libmoose-perl (2.0401-1) ... Setting up libarray-compare-perl (2.02-1) ... Setting up libvariable-magic-perl (0.47-1build1) ... Setting up libb-hooks-endofscope-perl (0.08-1) ... Setting up libbio-asn1-entrezgene-perl (1.091-2) ... Setting up libcarp-clan-perl (6.04-1) ... Setting up libbit-vector-perl (7.1-1build2) ... Setting up libclass-c3-xs-perl (0.13-1build2) ... Setting up libclass-inspector-perl (1.25-1) ... Setting up libclone-perl (0.31-1build3) ... Setting up libconvert-binary-c-perl (0.76-1build2) ... Setting up libconvert-binhex-perl (1.119+pristine-3) ... Setting up libcrypt-ssleay-perl (0.57-2ubuntu1) ... Setting up libdate-calc-perl (6.3-1) ... Setting up libdate-calc-xs-perl (6.2-1build1) ... Setting up libdate-manip-perl (6.25-1) ... Setting up libdbd-mysql-perl (4.020-1build2) ... Setting up libpq5 (9.1.11-0ubuntu0.12.04) ... Setting up libdbd-pg-perl (2.19.0-1) ... Setting up libdbd-sqlite3-perl (1.35-1) ... Setting up libsub-identify-perl (0.04-1build2) ... Setting up libnamespace-clean-perl (0.22-1) ... Setting up libdevel-partialdump-perl (0.15-1) ... Setting up libfcgi-perl (0.74-1build1) ... Setting up libfont-afm-perl (1.20-1) ... Setting up libfreezethaw-perl (0.5001-1) ... Setting up libheap-perl (0.80-2) ... Setting up libgraph-perl (1:0.91-1) ... Setting up libio-pty-perl (1:1.08-1build2) ... Setting up libipc-run-perl (0.90-1) ... Setting up libparse-recdescent-perl (1.965001+dfsg-1) ... Setting up libhtml-form-perl (6.00-1) ... Setting up libhtml-format-perl (2.10-1) ... Setting up libhttp-daemon-perl (6.00-1) ... Setting up libsocket6-perl (0.23-1build2) ... Setting up libio-socket-inet6-perl (2.69-2) ... Setting up libio-stringy-perl (2.110-5) ... Setting up libjcode-pm-perl (2.06-1) ... Setting up libmailtools-perl (2.08-1) ... Setting up libmath-derivative-perl (0.01-6) ... Setting up libmath-spline-perl (0.01-4) ... Setting up libmime-tools-perl (5.502-1) ... Setting up libmldbm-perl (2.04-1) ... Setting up libnetpbm10 (2:10.0-15) ... Setting up libole-storage-lite-perl (0.19-1) ... Setting up libossp-uuid16 (1.6.2-1.1build3) ... Setting up libossp-uuid-perl (1.6.2-1.1build3) ... Setting up libpostscript-perl (0.06-2) ... Setting up libsort-naturally-perl (1.02-1) ... Setting up libspreadsheet-writeexcel-perl (2.37-1) ... Setting up libunicode-map-perl (0.112-10build3) ... Setting up libspreadsheet-parseexcel-perl (0.5800-1) ... Setting up libstatistics-descriptive-perl (3.0203-1) ... Setting up libsvg-perl (2.50-1) ... Setting up libtree-dagnode-perl (1.06-1) ... Setting up libsvg-graph-perl (0.02-2) ... Setting up libtie-ixhash-perl (1.21-2) ... Setting up libxml-regexp-perl (0.03-8) ... Setting up libxml-xpathengine-perl (0.13-1) ... Setting up libxml-namespacesupport-perl (1.09-3) ... Setting up libxml-sax-base-perl (1.07-1) ... Setting up libxml-sax-perl (0.99+dfsg-1ubuntu0.1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-filter-buffertext-perl (1.01-5) ... Setting up libxml-libxml-perl (1.89+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxslt-perl (1.75-2) ... Setting up libxml-sax-writer-perl (0.53-1) ... Setting up libxml-simple-perl (2.18-3) ... Setting up libxml-writer-perl (0.612-1) ... Setting up libyaml-perl (0.77-1) ... Setting up maq (0.7.1-4) ... Setting up muscle (1:3.8.31-1) ... Setting up netpbm (2:10.0-15) ... Setting up perl-doc (5.14.2-6ubuntu2.4) ... Setting up perl-tk (1:804.029-1.1ubuntu2) ... Setting up phyml (2:20110919-1) ... Setting up primer3 (2.2.3-1) ... Setting up probcons (1.12-8) ... Setting up sim4 (0.0.20030921-3) ... Setting up t-coffee (9.03.r1318-1ubuntu2) ... Setting up tigr-glimmer (3.02-2build1) ... Setting up tm-align (20111012-1build1) ... Setting up tree-puzzle-doc (5.2-7) ... Setting up xaw3dg (1.5+E-18.1ubuntu1) ... Setting up xfig (1:3.2.5.b-2ubuntu1) ... Setting up xfig-libs (1:3.2.5.b-2ubuntu1) ... Setting up bowtie (1.0.0-1-0ubuntu2) ... Setting up libbsd-resource-perl (1.2904-1build2) ... Setting up libgd-gd2-perl (1:2.46-3build1) ... Setting up libset-scalar-perl (1.25-1) ... Setting up liblwp-protocol-https-perl (6.02-1) ... Setting up libwww-perl (6.03-1) ... Setting up libapache2-mod-perl2 (2.0.5-5ubuntu1) ... Enabling module perl. To activate the new configuration, you need to run: service apache2 restart Setting up libapache-dbi-perl (1.11-1) ... Setting up libapache2-reload-perl (0.11-2) ... Setting up libxml-parser-perl (2.41-1build1) ... Setting up libxml-twig-perl (1:3.39-1ubuntu1) ... Setting up libgraphviz-perl (2.04-1) ... Setting up libsoap-lite-perl (0.714-1) ... Setting up libxml-perl (0.08-2) ... Setting up libxml-dom-perl (1.44-1) ... Setting up libxml-dom-xpath-perl (0.14-1) ... Setting up libxml-sax-expat-perl (0.40-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::Expat with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-xpath-perl (1.13-7) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Reading package lists... Done Building dependency tree Reading state information... Done arb-doc is already the newest version. arb-doc set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded. Reading package lists... Done Building dependency tree Reading state information... Done The following NEW packages will be installed: beam2 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded. Need to get 381 kB of archives. After this operation, 851 kB of additional disk space will be used. Get:1 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ precise/main beam2 i386 0.1+20101008-1 [381 kB] Fetched 381 kB in 0s (753 kB/s) Selecting previously unselected package beam2. (Reading database ... 161954 files and directories currently installed.) Unpacking beam2 (from .../beam2_0.1+20101008-1_i386.deb) ... Setting up beam2 (0.1+20101008-1) ... Reading package lists... Done Building dependency tree Reading state information... Done The following NEW packages will be installed: bio-linux-ampliconnoise 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded. Need to get 20.0 kB of archives. After this operation, 2,048 kB of additional disk space will be used. Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-ampliconnoise all 1bl-0 [20.0 kB] Fetched 20.0 kB in 0s (198 kB/s) Selecting previously unselected package bio-linux-ampliconnoise. (Reading database ... 161959 files and directories currently installed.) Unpacking bio-linux-ampliconnoise (from .../bio-linux-ampliconnoise_1bl-0_all.deb) ... Setting up bio-linux-ampliconnoise (1bl-0) ... Reading package lists... Done Building dependency tree Reading state information... Done The following NEW packages will be installed: bio-linux-arb 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded. Need to get 3,534 B of archives. After this operation, 102 kB of additional disk space will be used. Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-arb all 1:1bl1-3 [3,534 B] Fetched 3,534 B in 0s (44.2 kB/s) Selecting previously unselected package bio-linux-arb. (Reading database ... 161993 files and directories currently installed.) Unpacking bio-linux-arb (from .../bio-linux-arb_1%3a1bl1-3_all.deb) ... Processing triggers for bamfdaemon ... Rebuilding /usr/share/applications/bamf.index... Processing triggers for desktop-file-utils ... Processing triggers for gnome-menus ... Setting up bio-linux-arb (1:1bl1-3) ... Reading package lists... Done Building dependency tree Reading state information... Done The following extra packages will be installed: ca-certificates-java icedtea-6-jre-cacao icedtea-6-jre-jamvm icedtea-netx icedtea-netx-common java-common libatk-wrapper-java libatk-wrapper-java-jni libgif4 libnss3-1d openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib ttf-dejavu-extra tzdata-java Suggested packages: default-jre equivs icedtea-plugin sun-java6-fonts fonts-ipafont-gothic fonts-ipafont-mincho ttf-telugu-fonts ttf-oriya-fonts ttf-kannada-fonts ttf-bengali-fonts The following NEW packages will be installed: bio-linux-archaeopteryx ca-certificates-java icedtea-6-jre-cacao icedtea-6-jre-jamvm icedtea-netx icedtea-netx-common java-common libatk-wrapper-java libatk-wrapper-java-jni libgif4 libnss3-1d openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib ttf-dejavu-extra tzdata-java 0 upgraded, 16 newly installed, 0 to remove and 14 not upgraded. Need to get 42.2 MB of archives. After this operation, 106 MB of additional disk space will be used. Get:1 http://dk.archive.ubuntu.com/ubuntu/ precise-updates/main openjdk-6-jre-lib all 6b27-1.12.6-1ubuntu0.12.04.4 [6,142 kB] Get:2 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-archaeopteryx all 0.972.beta9M-3 [2,659 kB] Get:3 http://dk.archive.ubuntu.com/ubuntu/ precise-updates/main libnss3-1d i386 3.15.4-0ubuntu0.12.04.1 [13.4 kB] Get:4 http://dk.archive.ubuntu.com/ubuntu/ precise/main ca-certificates-java all 20110912ubuntu6 [8,186 B] Get:5 http://dk.archive.ubuntu.com/ubuntu/ precise-updates/main tzdata-java all 2013g-0ubuntu0.12.04 [138 kB] Get:6 http://dk.archive.ubuntu.com/ubuntu/ precise/main java-common all 0.43ubuntu2 [61.7 kB] Get:7 http://dk.archive.ubuntu.com/ubuntu/ precise-updates/main openjdk-6-jre-headless i386 6b27-1.12.6-1ubuntu0.12.04.4 [27.5 MB] Get:8 http://dk.archive.ubuntu.com/ubuntu/ precise/main libgif4 i386 4.1.6-9ubuntu1 [31.2 kB] Get:9 http://dk.archive.ubuntu.com/ubuntu/ precise-updates/main openjdk-6-jre i386 6b27-1.12.6-1ubuntu0.12.04.4 [232 kB] Get:10 http://dk.archive.ubuntu.com/ubuntu/ precise/main libatk-wrapper-java all 0.30.4-0ubuntu2 [30.9 kB] Get:11 http://dk.archive.ubuntu.com/ubuntu/ precise/main libatk-wrapper-java-jni i386 0.30.4-0ubuntu2 [31.0 kB] Get:12 http://dk.archive.ubuntu.com/ubuntu/ precise/main ttf-dejavu-extra all 2.33-2ubuntu1 [3,420 kB] Get:13 http://dk.archive.ubuntu.com/ubuntu/ precise-updates/main icedtea-6-jre-cacao i386 6b27-1.12.6-1ubuntu0.12.04.4 [770 kB] Get:14 http://dk.archive.ubuntu.com/ubuntu/ precise-updates/main icedtea-6-jre-jamvm i386 6b27-1.12.6-1ubuntu0.12.04.4 [536 kB] Get:15 http://dk.archive.ubuntu.com/ubuntu/ precise-updates/main icedtea-netx-common all 1.2.3-0ubuntu0.12.04.3 [600 kB] Get:16 http://dk.archive.ubuntu.com/ubuntu/ precise-updates/main icedtea-netx i386 1.2.3-0ubuntu0.12.04.3 [16.2 kB] Fetched 42.2 MB in 5s (8,343 kB/s) Selecting previously unselected package openjdk-6-jre-lib. (Reading database ... 161995 files and directories currently installed.) Unpacking openjdk-6-jre-lib (from .../openjdk-6-jre-lib_6b27-1.12.6-1ubuntu0.12.04.4_all.deb) ... Selecting previously unselected package libnss3-1d. Unpacking libnss3-1d (from .../libnss3-1d_3.15.4-0ubuntu0.12.04.1_i386.deb) ... Selecting previously unselected package ca-certificates-java. Unpacking ca-certificates-java (from .../ca-certificates-java_20110912ubuntu6_all.deb) ... Selecting previously unselected package tzdata-java. Unpacking tzdata-java (from .../tzdata-java_2013g-0ubuntu0.12.04_all.deb) ... Selecting previously unselected package java-common. Unpacking java-common (from .../java-common_0.43ubuntu2_all.deb) ... Selecting previously unselected package openjdk-6-jre-headless. Unpacking openjdk-6-jre-headless (from .../openjdk-6-jre-headless_6b27-1.12.6-1ubuntu0.12.04.4_i386.deb) ... Selecting previously unselected package libgif4. Unpacking libgif4 (from .../libgif4_4.1.6-9ubuntu1_i386.deb) ... Selecting previously unselected package openjdk-6-jre. Unpacking openjdk-6-jre (from .../openjdk-6-jre_6b27-1.12.6-1ubuntu0.12.04.4_i386.deb) ... Selecting previously unselected package libatk-wrapper-java. Unpacking libatk-wrapper-java (from .../libatk-wrapper-java_0.30.4-0ubuntu2_all.deb) ... Selecting previously unselected package libatk-wrapper-java-jni. Unpacking libatk-wrapper-java-jni (from .../libatk-wrapper-java-jni_0.30.4-0ubuntu2_i386.deb) ... Selecting previously unselected package bio-linux-archaeopteryx. Unpacking bio-linux-archaeopteryx (from .../bio-linux-archaeopteryx_0.972.beta9M-3_all.deb) ... Selecting previously unselected package ttf-dejavu-extra. Unpacking ttf-dejavu-extra (from .../ttf-dejavu-extra_2.33-2ubuntu1_all.deb) ... Selecting previously unselected package icedtea-6-jre-cacao. Unpacking icedtea-6-jre-cacao (from .../icedtea-6-jre-cacao_6b27-1.12.6-1ubuntu0.12.04.4_i386.deb) ... Selecting previously unselected package icedtea-6-jre-jamvm. Unpacking icedtea-6-jre-jamvm (from .../icedtea-6-jre-jamvm_6b27-1.12.6-1ubuntu0.12.04.4_i386.deb) ... Selecting previously unselected package icedtea-netx-common. Unpacking icedtea-netx-common (from .../icedtea-netx-common_1.2.3-0ubuntu0.12.04.3_all.deb) ... Selecting previously unselected package icedtea-netx. Unpacking icedtea-netx (from .../icedtea-netx_1.2.3-0ubuntu0.12.04.3_i386.deb) ... Processing triggers for doc-base ... Processing 2 added doc-base files... Processing triggers for man-db ... Processing triggers for bamfdaemon ... Rebuilding /usr/share/applications/bamf.index... Processing triggers for desktop-file-utils ... Processing triggers for gnome-menus ... Processing triggers for hicolor-icon-theme ... Processing triggers for fontconfig ... Setting up libnss3-1d (3.15.4-0ubuntu0.12.04.1) ... Setting up tzdata-java (2013g-0ubuntu0.12.04) ... Setting up java-common (0.43ubuntu2) ... Setting up libgif4 (4.1.6-9ubuntu1) ... Setting up ttf-dejavu-extra (2.33-2ubuntu1) ... Setting up icedtea-netx-common (1.2.3-0ubuntu0.12.04.3) ... Setting up openjdk-6-jre-headless (6b27-1.12.6-1ubuntu0.12.04.4) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/java to provide /usr/bin/java (java) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode. Setting up ca-certificates-java (20110912ubuntu6) ... Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Adding debian:Comodo_Secure_Services_root.pem Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem Adding debian:TC_TrustCenter_Universal_CA_I.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Certigna.pem Adding debian:ComSign_CA.pem Adding debian:Certinomis_-_Autorit?_Racine.pem Adding debian:spi-ca-2003.pem Adding debian:SwissSign_Platinum_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Equifax_Secure_eBusiness_CA_2.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:AddTrust_Low-Value_Services_Root.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Equifax_Secure_CA.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:ApplicationCA_-_Japanese_Government.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Thawte_Premium_Server_CA.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_3.pem Adding debian:TC_TrustCenter_Universal_CA_III.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:cacert.org.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Camerfirma_Global_Chambersign_Root.pem Adding debian:A-Trust-nQual-03.pem Adding debian:NetLock_Express_=Class_C=_Root.pem Adding debian:T?B?TAK_UEKAE_K?k_Sertifika_Hizmet_Sa?lay?c?s?_-_S?r?m_3.pem Adding debian:IGC_A.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:NetLock_Qualified_=Class_QA=_Root.pem Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sa?lay?c?s?.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:TDC_OCES_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:UbuntuOne-Go_Daddy_Class_2_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:UbuntuOne-Go_Daddy_CA.pem Adding debian:NetLock_Business_=Class_B=_Root.pem Adding debian:DST_ACES_CA_X6.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Adding debian:ca.pem Adding debian:AddTrust_Public_Services_Root.pem Adding debian:Swisscom_Root_CA_1.pem Adding debian:Firmaprofesional_Root_CA.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:TC_TrustCenter_Class_2_CA_II.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:NetLock_Arany_=Class_Gold=_F?tan?s?tv?ny.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:RSA_Root_Certificate_1.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Taiwan_GRCA.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Verisign_Class_4_Public_Primary_Certification_Authority_-_G2.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Comodo_Trusted_Services_root.pem Adding debian:Root_CA_Generalitat_Valenciana.pem Adding debian:America_Online_Root_Certification_Authority_2.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Microsec_e-Szigno_Root_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:AddTrust_Qualified_Certificates_Root.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_1.pem Adding debian:Equifax_Secure_Global_eBusiness_CA.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Adding debian:ssl-cert-snakeoil.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_1.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Secure_Global_CA.pem Adding debian:UTN_DATACorp_SGC_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:NetLock_Notary_=Class_A=_Root.pem Adding debian:Wells_Fargo_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Security_Communication_EV_RootCA1.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:TC_TrustCenter__Germany__Class_2_CA.pem Adding debian:GTE_CyberTrust_Global_Root.pem Adding debian:AC_Ra?z_Certic?mara_S.A..pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:CNNIC_ROOT.pem Adding debian:RSA_Security_2048_v3.pem Adding debian:ValiCert_Class_2_VA.pem Adding debian:TDC_Internet_Root_CA.pem Adding debian:TC_TrustCenter__Germany__Class_3_CA.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:GeoTrust_Global_CA_2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:Buypass_Class_2_CA_1.pem Adding debian:Certum_Root_CA.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:Sonera_Class_1_Root_CA.pem Adding debian:Entrust.net_Secure_Server_CA.pem Adding debian:Verisign_Class_4_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Buypass_Class_3_CA_1.pem Adding debian:E-Guven_Kok_Elektronik_Sertifika_Hizmet_Saglayicisi.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Adding debian:Equifax_Secure_eBusiness_CA_1.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:spi-cacert-2008.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem Adding debian:ValiCert_Class_1_VA.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:TC_TrustCenter_Class_3_CA_II.pem Adding debian:Staat_der_Nederlanden_Root_CA.pem Adding debian:ACEDICOM_Root.pem Adding debian:ComSign_Secured_CA.pem Adding debian:CA_Disig.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Izenpe.com.pem Adding debian:AddTrust_External_Root.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:UTN_USERFirst_Email_Root_CA.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:StartCom_Certification_Authority.pem Adding debian:Juur-SK.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:America_Online_Root_Certification_Authority_1.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:SecureTrust_CA.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:UTN_USERFirst_Hardware_Root_CA.pem Adding debian:Thawte_Server_CA.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority.pem done. Setting up libatk-wrapper-java (0.30.4-0ubuntu2) ... Setting up icedtea-6-jre-cacao (6b27-1.12.6-1ubuntu0.12.04.4) ... Setting up icedtea-6-jre-jamvm (6b27-1.12.6-1ubuntu0.12.04.4) ... Setting up openjdk-6-jre-lib (6b27-1.12.6-1ubuntu0.12.04.4) ... Setting up libatk-wrapper-java-jni (0.30.4-0ubuntu2) ... Setting up openjdk-6-jre (6b27-1.12.6-1ubuntu0.12.04.4) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode. Setting up bio-linux-archaeopteryx (0.972.beta9M-3) ... Setting up icedtea-netx (1.2.3-0ubuntu0.12.04.3) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/javaws to provide /usr/bin/javaws (javaws) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/itweb-settings to provide /usr/bin/itweb-settings (itweb-settings) in auto mode. Processing triggers for libc-bin ... ldconfig deferred processing now taking place Reading package lists... Done Building dependency tree Reading state information... Done The following NEW packages will be installed: bio-linux-artemis 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded. Need to get 11.8 MB of archives. After this operation, 47.7 MB of additional disk space will be used. Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-artemis all 15.1.1-1 [11.8 MB] Fetched 11.8 MB in 2s (5,111 kB/s) Selecting previously unselected package bio-linux-artemis. (Reading database ... 162928 files and directories currently installed.) Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.deb) ... Processing triggers for bamfdaemon ... Rebuilding /usr/share/applications/bamf.index... Processing triggers for desktop-file-utils ... Processing triggers for gnome-menus ... Setting up bio-linux-artemis (15.1.1-1) ... Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package bio-linux-assembly-conversion-tools Not all packages installed properly - exiting. From tony.travis at abdn.ac.uk Thu Feb 13 10:47:38 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Thu, 13 Feb 2014 15:47:38 +0000 Subject: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: References: <1392144869.5335.3.camel@balisaur> <52FB942B.8070103@abdn.ac.uk> Message-ID: <52FCE91A.3070001@abdn.ac.uk> On 13/02/14 15:06, Jasmine Lognnes wrote: > Dear Tony, > > That is good news. I have now tried it on a fresh Ubuntu 12.04 64bit, > and it exits with pasted in at the bottom. More complete output attached. > > What can you gather from this? Hi, Jasmine. Tim's advice is to run his upgrade script again if it crashes because of broken dependencies. I use "aptitude" to correct any inconsistencies in APT because it is good at fixing broken dependencies: # get a root shell sudo -i # install aptitude apt-get update apt-get install aptitude # fix broken dependencies aptitude -f install # make sure everything is up-to-date aptitude dist-upgrade # check if the package is available apt-cache policy bio-linux-assembly-conversion-tools bio-linux-assembly-conversion-tools: Installed: 0.01-10 Candidate: 0.01-10 Version table: *** 0.01-10 0 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages 100 /var/lib/dpkg/status # re-run Tim's script bash bl_do_update_to7.sh If you can't get it to work, check your APT configuration has the attached files in it. If not, copy them in and update APT: aptitude update I've upgraded quite a few Ubuntu servers to Bio-Linux using Tim's script and it works quite well if you make sure you keep your APT consistent using "aptitude" as I've described. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. -------------- next part -------------- # Packages from PPA deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main # Packages from Bio-Linux main repo. Note that adding this repo # without the above PPA will result in some missing dependencies, so # don't do that! deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux # Don't try to add a matching deb-src line to the above. There is no # source repo. If we have source, it's in the PPA. -------------- next part -------------- deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/ deb-src http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/ From princess.jasmine.lognnes at gmail.com Fri Feb 14 05:29:01 2014 From: princess.jasmine.lognnes at gmail.com (Jasmine Lognnes) Date: Fri, 14 Feb 2014 11:29:01 +0100 Subject: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: References: <1392144869.5335.3.camel@balisaur> <52FB942B.8070103@abdn.ac.uk> Message-ID: Dear Tony, That is good news. I have now tried it on a fresh Ubuntu 12.04 64bit, and it exits with pasted in at the bottom. What can you gather from this? Hugs, Jasmine =) The following NEW packages will be installed: bio-linux-artemis 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded. Need to get 11.8 MB of archives. After this operation, 47.7 MB of additional disk space will be used. Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-artemis all 15.1.1-1 [11.8 MB] Fetched 11.8 MB in 2s (5,111 kB/s) Selecting previously unselected package bio-linux-artemis. (Reading database ... 162928 files and directories currently installed.) Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.deb) ... Processing triggers for bamfdaemon ... Rebuilding /usr/share/applications/bamf.index... Processing triggers for desktop-file-utils ... Processing triggers for gnome-menus ... Setting up bio-linux-artemis (15.1.1-1) ... Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package bio-linux-assembly-conversion-tools Not all packages installed properly - exiting. On 12 February 2014 16:32, Tony Travis wrote: > > On 12/02/14 15:03, Jasmine Lognnes wrote: > > Dear Tim, > > > > That's a very impressive script. Wow! > > > > By going through the script I have cherry picked what looks like to be > > needed on a plain Ubuntu 12.04 64bit. I have attached it as a script. > > Can you verify that it is the correct procedure? > > > > On the liveUSB I did > > > > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}' > > > > and got the attached list of packages. On a successful installation, > > should I end up these exact packages? > > Hi, Jasmine. > > I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu > 12.04 LTS systems without any problems. You don't need to grep things > out like you did. Just run the script in its entirety and please email > any bug reports to the bio-linux-dev list. > > HTH, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > The University of Aberdeen is a charity registered in Scotland, No SC013683. > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From Jan-Hendrik.Troesemeier at pei.de Fri Feb 14 07:38:04 2014 From: Jan-Hendrik.Troesemeier at pei.de (Troesemeier, Jan-Hendrik) Date: Fri, 14 Feb 2014 12:38:04 +0000 Subject: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: References: <1392144869.5335.3.camel@balisaur> <52FB942B.8070103@abdn.ac.uk> Message-ID: <7315882635848A4DA04855A825AFC76A59A515F5@sv-exch-02.ad.pei.de> Dear Jasmine, have you added the biolinux repositories (e.g. explained in http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository )? Afaik the missing package is a biolinux-repo only one. Cheers, jan -----Urspr?ngliche Nachricht----- Von: Jasmine Lognnes [mailto:princess.jasmine.lognnes at gmail.com] Gesendet: Freitag, 14. Februar 2014 11:29 An: Bio-Linux help and discussion Cc: Bio-Linux technical discussion Betreff: Re: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? Dear Tony, That is good news. I have now tried it on a fresh Ubuntu 12.04 64bit, and it exits with pasted in at the bottom. What can you gather from this? Hugs, Jasmine =) The following NEW packages will be installed: bio-linux-artemis 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded. Need to get 11.8 MB of archives. After this operation, 47.7 MB of additional disk space will be used. Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-artemis all 15.1.1-1 [11.8 MB] Fetched 11.8 MB in 2s (5,111 kB/s) Selecting previously unselected package bio-linux-artemis. (Reading database ... 162928 files and directories currently installed.) Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.deb) ... Processing triggers for bamfdaemon ... Rebuilding /usr/share/applications/bamf.index... Processing triggers for desktop-file-utils ... Processing triggers for gnome-menus ... Setting up bio-linux-artemis (15.1.1-1) ... Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package bio-linux-assembly-conversion-tools Not all packages installed properly - exiting. On 12 February 2014 16:32, Tony Travis wrote: > > On 12/02/14 15:03, Jasmine Lognnes wrote: > > Dear Tim, > > > > That's a very impressive script. Wow! > > > > By going through the script I have cherry picked what looks like to > > be needed on a plain Ubuntu 12.04 64bit. I have attached it as a script. > > Can you verify that it is the correct procedure? > > > > On the liveUSB I did > > > > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}' > > > > and got the attached list of packages. On a successful installation, > > should I end up these exact packages? > > Hi, Jasmine. > > I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu > 12.04 LTS systems without any problems. You don't need to grep things > out like you did. Just run the script in its entirety and please email > any bug reports to the bio-linux-dev list. > > HTH, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, > Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > The University of Aberdeen is a charity registered in Scotland, No SC013683. > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux _______________________________________________ Bio-Linux-dev mailing list Bio-Linux-dev at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev From princess.jasmine.lognnes at gmail.com Fri Feb 14 07:51:30 2014 From: princess.jasmine.lognnes at gmail.com (Jasmine Lognnes) Date: Fri, 14 Feb 2014 13:51:30 +0100 Subject: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: <7315882635848A4DA04855A825AFC76A59A515F5@sv-exch-02.ad.pei.de> References: <1392144869.5335.3.camel@balisaur> <52FB942B.8070103@abdn.ac.uk> <7315882635848A4DA04855A825AFC76A59A515F5@sv-exch-02.ad.pei.de> Message-ID: Dear Jan, The script added those for me, but looking at the repos in a browser, I can't see the bio-linux-assembly-conversion-tools in any of the repos. apt-cache search bio-linux | assembly doesn't give any hits either. However I see the package installed on the liveUSB stick. Have it been made from another repo? Hugs, Jasmine =) On 14 February 2014 13:38, Troesemeier, Jan-Hendrik wrote: > Dear Jasmine, > > have you added the biolinux repositories (e.g. explained in http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository )? Afaik the missing package is a biolinux-repo only one. > > Cheers, > jan > > -----Urspr?ngliche Nachricht----- > Von: Jasmine Lognnes [mailto:princess.jasmine.lognnes at gmail.com] > Gesendet: Freitag, 14. Februar 2014 11:29 > An: Bio-Linux help and discussion > Cc: Bio-Linux technical discussion > Betreff: Re: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? > > Dear Tony, > > That is good news. I have now tried it on a fresh Ubuntu 12.04 64bit, and it exits with pasted in at the bottom. What can you gather from this? > > Hugs, > Jasmine =) > > > > The following NEW packages will be installed: > bio-linux-artemis > 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded. > Need to get 11.8 MB of archives. > After this operation, 47.7 MB of additional disk space will be used. > Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-artemis all 15.1.1-1 [11.8 MB] Fetched 11.8 MB in 2s (5,111 kB/s) Selecting previously unselected package bio-linux-artemis. > (Reading database ... 162928 files and directories currently installed.) Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.deb) ... > Processing triggers for bamfdaemon ... > Rebuilding /usr/share/applications/bamf.index... > Processing triggers for desktop-file-utils ... > Processing triggers for gnome-menus ... > Setting up bio-linux-artemis (15.1.1-1) ... > Reading package lists... Done > Building dependency tree > Reading state information... Done > E: Unable to locate package bio-linux-assembly-conversion-tools > Not all packages installed properly - exiting. > > > > > > > > On 12 February 2014 16:32, Tony Travis wrote: >> >> On 12/02/14 15:03, Jasmine Lognnes wrote: >> > Dear Tim, >> > >> > That's a very impressive script. Wow! >> > >> > By going through the script I have cherry picked what looks like to >> > be needed on a plain Ubuntu 12.04 64bit. I have attached it as a script. >> > Can you verify that it is the correct procedure? >> > >> > On the liveUSB I did >> > >> > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}' >> > >> > and got the attached list of packages. On a successful installation, >> > should I end up these exact packages? >> >> Hi, Jasmine. >> >> I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu >> 12.04 LTS systems without any problems. You don't need to grep things >> out like you did. Just run the script in its entirety and please email >> any bug reports to the bio-linux-dev list. >> >> HTH, >> >> Tony. >> >> -- >> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and >> Environmental Sciences, Cruickshank Building, St. Machar Drive, >> Aberdeen >> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 >> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis >> The University of Aberdeen is a charity registered in Scotland, No SC013683. >> _______________________________________________ >> Bio-Linux mailing list >> Bio-Linux at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev From tony.travis at abdn.ac.uk Fri Feb 14 08:07:54 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Fri, 14 Feb 2014 13:07:54 +0000 Subject: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: References: <1392144869.5335.3.camel@balisaur> <52FB942B.8070103@abdn.ac.uk> <7315882635848A4DA04855A825AFC76A59A515F5@sv-exch-02.ad.pei.de> Message-ID: <52FE152A.8090709@abdn.ac.uk> On 14/02/14 12:51, Jasmine Lognnes wrote: > Dear Jan, > > The script added those for me, but looking at the repos in a browser, > I can't see the bio-linux-assembly-conversion-tools in any of the > repos. apt-cache search bio-linux | assembly doesn't give any hits > either. > > However I see the package installed on the liveUSB stick. Have it been > made from another repo? Hi, Jasmine. I'm using the sources.list fragment I sent you on my laptop "beluga": > ajt at beluga:~$ cat /etc/apt/sources.list.d/nebc-bio-linux-precise.list > # Packages from PPA > deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main > deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main > > # Packages from Bio-Linux main repo. Note that adding this repo > # without the above PPA will result in some missing dependencies, so > # don't do that! > deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux > > # Don't try to add a matching deb-src line to the above. There is no > # source repo. If we have source, it's in the PPA. I've already got "bio-linux-assembly-conversion-tools" installed and this is the APT policy for it: > ajt at beluga:~$ apt-cache policy bio-linux-assembly-conversion-tools > bio-linux-assembly-conversion-tools: > Installed: 0.01-10 > Candidate: 0.01-10 > Version table: > *** 0.01-10 0 > 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages > 100 /var/lib/dpkg/status I can remove "bio-linux-assembly-conversion-tools" and re-install it without any problems, so there is nothing wrong with the repository: > ajt at beluga:~$ sudo aptitude purge bio-linux-assembly-conversion-tools > The following packages will be REMOVED: > bio-linux-assembly-conversion-tools{p} bio-linux-staden{u} > 0 packages upgraded, 0 newly installed, 2 to remove and 0 not upgraded. > Need to get 0 B of archives. After unpacking 131 MB will be freed. > Do you want to continue? [Y/n/?] > (Reading database ... 847007 files and directories currently installed.) > Removing bio-linux-assembly-conversion-tools ... > Purging configuration files for bio-linux-assembly-conversion-tools ... > (Reading database ... 846664 files and directories currently installed.) > Removing bio-linux-staden ... > Processing triggers for bamfdaemon ... > Rebuilding /usr/share/applications/bamf.index... > Processing triggers for desktop-file-utils ... > Processing triggers for gnome-menus ... This removed any cached copy of the package on my laptop: > ajt at beluga:~$ sudo aptitude clean Now, re-install from scratch: > ajt at beluga:~$ sudo aptitude install bio-linux-assembly-conversion-tools > The following NEW packages will be installed: > bio-linux-assembly-conversion-tools bio-linux-staden{a} > 0 packages upgraded, 2 newly installed, 0 to remove and 0 not upgraded. > Need to get 52.3 MB of archives. After unpacking 131 MB will be used. > Do you want to continue? [Y/n/?] > Get: 1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-staden amd64 2006.1.7.0+1.11.6-7 [45.9 MB] > Get: 2 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-assembly-conversion-tools amd64 0.01-10 [6,335 kB] > Fetched 52.3 MB in 16s (3,154 kB/s) > Selecting previously unselected package bio-linux-staden. > (Reading database ... 843364 files and directories currently installed.) > Unpacking bio-linux-staden (from .../bio-linux-staden_2006.1.7.0+1.11.6-7_amd64.deb) ... > Selecting previously unselected package bio-linux-assembly-conversion-tools. > Unpacking bio-linux-assembly-conversion-tools (from .../bio-linux-assembly-conversion-tools_0.01-10_amd64.deb) ... > Processing triggers for bamfdaemon ... > Rebuilding /usr/share/applications/bamf.index... > Processing triggers for desktop-file-utils ... > Processing triggers for gnome-menus ... > Setting up bio-linux-staden (2006.1.7.0+1.11.6-7) ... > Setting up bio-linux-assembly-conversion-tools (0.01-10) ... Try installing it manually (i.e. not by running Tim's script): sudo -i apt-get update apt-get install aptitude aptitude -f install aptitude install bio-linux-assembly-conversion-tools HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. From tony.travis at abdn.ac.uk Fri Feb 14 08:13:29 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Fri, 14 Feb 2014 13:13:29 +0000 Subject: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: References: <1392144869.5335.3.camel@balisaur> <52FB942B.8070103@abdn.ac.uk> <7315882635848A4DA04855A825AFC76A59A515F5@sv-exch-02.ad.pei.de> Message-ID: <52FE1679.8050805@abdn.ac.uk> On 14/02/14 12:51, Jasmine Lognnes wrote: > Dear Jan, > > The script added those for me, but looking at the repos in a browser, > I can't see the bio-linux-assembly-conversion-tools in any of the > repos. apt-cache search bio-linux | assembly doesn't give any hits > either. Hi, Jasmine. I guess you meant to pipe the output through "fgrep": > ajt at beluga:~$ apt-cache search bio-linux | fgrep assembly > bio-linux-assembly-conversion-tools - Conversion tools for handling 454 assemblies. > bio-linux-lucy - Preparation of raw DNA sequence fragments for sequence assembly. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. From tbooth at ceh.ac.uk Fri Feb 14 09:15:40 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 14 Feb 2014 14:15:40 +0000 Subject: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: References: <1392144869.5335.3.camel@balisaur> <52FB942B.8070103@abdn.ac.uk> <7315882635848A4DA04855A825AFC76A59A515F5@sv-exch-02.ad.pei.de> Message-ID: <1392387340.21606.58.camel@balisaur> Hi Jasmine, Kudos to you for persisting on this. APT is awesome when it works, but infuriating when it doesn't. As you've probably now realised, the packages come in several categories: bio-linux-* packages that you want to install packages that come directly from Ubuntu packages that sit in the Bio-Linux PPA packages that come from other sources (eg. CRAN) a few bio-linux-* packages that you probably don't want to install I'm always trying to tidy up the situation by moving packages to the PPA but some just won't go. The big update script is supposed to sort it all out for you in any case. Your error is curious because you seem to be getting the "all" architecture packages (artemis) but not the "amd64" packages (assembly-conversion-tools). You can see that bio-linux-assembly-conversion tools really is there on the repo: http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-amd64/Packages Normally I'd guess this means you have 32-bit Ubuntu but you say you definitely have 64-bit installed. Nevertheless it could be some APT configuration issue that is stopping it picking up the binary packages. Can you please send the output of: apt-config dump Cheers, TIM On Fri, 2014-02-14 at 12:51 +0000, Jasmine Lognnes wrote: > Dear Jan, > > The script added those for me, but looking at the repos in a browser, > I can't see the bio-linux-assembly-conversion-tools in any of the > repos. apt-cache search bio-linux | assembly doesn't give any hits > either. > > However I see the package installed on the liveUSB stick. Have it been > made from another repo? > > Hugs, > Jasmine =) > > > > > > > > On 14 February 2014 13:38, Troesemeier, Jan-Hendrik > wrote: > > Dear Jasmine, > > > > have you added the biolinux repositories (e.g. explained in http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository )? Afaik the missing package is a biolinux-repo only one. > > > > Cheers, > > jan > > > > -----Urspr?ngliche Nachricht----- > > Von: Jasmine Lognnes [mailto:princess.jasmine.lognnes at gmail.com] > > Gesendet: Freitag, 14. Februar 2014 11:29 > > An: Bio-Linux help and discussion > > Cc: Bio-Linux technical discussion > > Betreff: Re: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? > > > > Dear Tony, > > > > That is good news. I have now tried it on a fresh Ubuntu 12.04 64bit, and it exits with pasted in at the bottom. What can you gather from this? > > > > Hugs, > > Jasmine =) > > > > > > > > The following NEW packages will be installed: > > bio-linux-artemis > > 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded. > > Need to get 11.8 MB of archives. > > After this operation, 47.7 MB of additional disk space will be used. > > Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-artemis all 15.1.1-1 [11.8 MB] Fetched 11.8 MB in 2s (5,111 kB/s) Selecting previously unselected package bio-linux-artemis. > > (Reading database ... 162928 files and directories currently installed.) Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.deb) ... > > Processing triggers for bamfdaemon ... > > Rebuilding /usr/share/applications/bamf.index... > > Processing triggers for desktop-file-utils ... > > Processing triggers for gnome-menus ... > > Setting up bio-linux-artemis (15.1.1-1) ... > > Reading package lists... Done > > Building dependency tree > > Reading state information... Done > > E: Unable to locate package bio-linux-assembly-conversion-tools > > Not all packages installed properly - exiting. > > > > > > > > > > > > > > > > On 12 February 2014 16:32, Tony Travis wrote: > >> > >> On 12/02/14 15:03, Jasmine Lognnes wrote: > >> > Dear Tim, > >> > > >> > That's a very impressive script. Wow! > >> > > >> > By going through the script I have cherry picked what looks like to > >> > be needed on a plain Ubuntu 12.04 64bit. I have attached it as a script. > >> > Can you verify that it is the correct procedure? > >> > > >> > On the liveUSB I did > >> > > >> > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}' > >> > > >> > and got the attached list of packages. On a successful installation, > >> > should I end up these exact packages? > >> > >> Hi, Jasmine. > >> > >> I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu > >> 12.04 LTS systems without any problems. You don't need to grep things > >> out like you did. Just run the script in its entirety and please email > >> any bug reports to the bio-linux-dev list. > >> > >> HTH, > >> > >> Tony. > >> > >> -- > >> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > >> Environmental Sciences, Cruickshank Building, St. Machar Drive, > >> Aberdeen > >> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > >> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > >> The University of Aberdeen is a charity registered in Scotland, No SC013683. > >> _______________________________________________ > >> Bio-Linux mailing list > >> Bio-Linux at nebclists.nerc.ac.uk > >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > _______________________________________________ > > Bio-Linux-dev mailing list > > Bio-Linux-dev at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > > _______________________________________________ > > Bio-Linux-dev mailing list > > Bio-Linux-dev at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From princess.jasmine.lognnes at gmail.com Fri Feb 14 10:25:27 2014 From: princess.jasmine.lognnes at gmail.com (Jasmine Lognnes) Date: Fri, 14 Feb 2014 16:25:27 +0100 Subject: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: <52FE152A.8090709@abdn.ac.uk> References: <1392144869.5335.3.camel@balisaur> <52FB942B.8070103@abdn.ac.uk> <7315882635848A4DA04855A825AFC76A59A515F5@sv-exch-02.ad.pei.de> <52FE152A.8090709@abdn.ac.uk> Message-ID: Dear Tony and Tim, Thanks a lot for the very detailed help! The problem was indeed that my other laptop were only 32bit, and that was the one where I ran the upgrade script =) On my main laptop was where I tried to install all the packages =) So after a reinstall on the 64bit laptop, and running the upgrade script, it worked perfectly. Thanks a lot, and have a great weekend =) Hugs, Jasmine =) On 14 February 2014 14:07, Tony Travis wrote: > On 14/02/14 12:51, Jasmine Lognnes wrote: >> Dear Jan, >> >> The script added those for me, but looking at the repos in a browser, >> I can't see the bio-linux-assembly-conversion-tools in any of the >> repos. apt-cache search bio-linux | assembly doesn't give any hits >> either. >> >> However I see the package installed on the liveUSB stick. Have it been >> made from another repo? > > Hi, Jasmine. > > I'm using the sources.list fragment I sent you on my laptop "beluga": > >> ajt at beluga:~$ cat /etc/apt/sources.list.d/nebc-bio-linux-precise.list >> # Packages from PPA >> deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main >> deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main >> >> # Packages from Bio-Linux main repo. Note that adding this repo >> # without the above PPA will result in some missing dependencies, so >> # don't do that! >> deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux >> >> # Don't try to add a matching deb-src line to the above. There is no >> # source repo. If we have source, it's in the PPA. > > I've already got "bio-linux-assembly-conversion-tools" installed and > this is the APT policy for it: > >> ajt at beluga:~$ apt-cache policy bio-linux-assembly-conversion-tools >> bio-linux-assembly-conversion-tools: >> Installed: 0.01-10 >> Candidate: 0.01-10 >> Version table: >> *** 0.01-10 0 >> 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages >> 100 /var/lib/dpkg/status > > I can remove "bio-linux-assembly-conversion-tools" and re-install it > without any problems, so there is nothing wrong with the repository: > >> ajt at beluga:~$ sudo aptitude purge bio-linux-assembly-conversion-tools >> The following packages will be REMOVED: >> bio-linux-assembly-conversion-tools{p} bio-linux-staden{u} >> 0 packages upgraded, 0 newly installed, 2 to remove and 0 not upgraded. >> Need to get 0 B of archives. After unpacking 131 MB will be freed. >> Do you want to continue? [Y/n/?] >> (Reading database ... 847007 files and directories currently installed.) >> Removing bio-linux-assembly-conversion-tools ... >> Purging configuration files for bio-linux-assembly-conversion-tools ... >> (Reading database ... 846664 files and directories currently installed.) >> Removing bio-linux-staden ... >> Processing triggers for bamfdaemon ... >> Rebuilding /usr/share/applications/bamf.index... >> Processing triggers for desktop-file-utils ... >> Processing triggers for gnome-menus ... > > This removed any cached copy of the package on my laptop: > >> ajt at beluga:~$ sudo aptitude clean > > Now, re-install from scratch: > >> ajt at beluga:~$ sudo aptitude install bio-linux-assembly-conversion-tools >> The following NEW packages will be installed: >> bio-linux-assembly-conversion-tools bio-linux-staden{a} >> 0 packages upgraded, 2 newly installed, 0 to remove and 0 not upgraded. >> Need to get 52.3 MB of archives. After unpacking 131 MB will be used. >> Do you want to continue? [Y/n/?] >> Get: 1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-staden amd64 2006.1.7.0+1.11.6-7 [45.9 MB] >> Get: 2 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-assembly-conversion-tools amd64 0.01-10 [6,335 kB] >> Fetched 52.3 MB in 16s (3,154 kB/s) >> Selecting previously unselected package bio-linux-staden. >> (Reading database ... 843364 files and directories currently installed.) >> Unpacking bio-linux-staden (from .../bio-linux-staden_2006.1.7.0+1.11.6-7_amd64.deb) ... >> Selecting previously unselected package bio-linux-assembly-conversion-tools. >> Unpacking bio-linux-assembly-conversion-tools (from .../bio-linux-assembly-conversion-tools_0.01-10_amd64.deb) ... >> Processing triggers for bamfdaemon ... >> Rebuilding /usr/share/applications/bamf.index... >> Processing triggers for desktop-file-utils ... >> Processing triggers for gnome-menus ... >> Setting up bio-linux-staden (2006.1.7.0+1.11.6-7) ... >> Setting up bio-linux-assembly-conversion-tools (0.01-10) ... > > Try installing it manually (i.e. not by running Tim's script): > > sudo -i > apt-get update > apt-get install aptitude > aptitude -f install > aptitude install bio-linux-assembly-conversion-tools > > HTH, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > The University of Aberdeen is a charity registered in Scotland, No SC013683. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev From tony.travis at abdn.ac.uk Fri Feb 28 07:07:38 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Fri, 28 Feb 2014 12:07:38 +0000 Subject: [Bio-linux-dev] Corruption of persistent filesystem on USB-stick Message-ID: <53107C0A.8020608@abdn.ac.uk> Hi, Tim. I've had problems with filesystem corruption on USB-sticks created from your 7.0.9 and 7.1.0 Bio-Linux iso images. At first, I thought it was because I used an old USB-stick, but when I did a r/w test of the raw device it showed no errors. However, when I tried to use the 'portable' VirtualBox to 'virtualise' the 7.1.0 stick it complained about my USB "casper-rw" being larger than 4GiB, which is the maximum file size on a FAT32 partition - That made me wonder if the filesystem corruption was caused by "casper-rw" being larger than 4GiB on an 8GiB USB-stick? The maximum 'legal' file size for FAT 32 is: 2^32 - 1 = 4294967296 -1 bytes = 4GiB - 1 byte On my 8GiB sticks, "bio-linux-usb-maker" creates a "casper-rw" > 4GiB. This patch limits the size of "casper-rw" to 4095MiB, which is the largest file size that can be stored 'correctly' on the Bio-Linux USB-stick FAT32 filesystem. I don't know yet if it will solve the "casper-rw" corruption problem or not - I'll let you know after I've done some further testing of USB-sticks made from your 7.1.0 iso. Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. -------------- next part -------------- A non-text attachment was scrubbed... Name: bio-linux-usb-maker.patch Type: text/x-patch Size: 1828 bytes Desc: not available URL: From tbooth at ceh.ac.uk Fri Feb 28 08:51:05 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 28 Feb 2014 13:51:05 +0000 Subject: [Bio-linux-dev] Corruption of persistent filesystem on USB-stick In-Reply-To: <53107C0A.8020608@abdn.ac.uk> References: <53107C0A.8020608@abdn.ac.uk> Message-ID: <1393595465.10237.356.camel@balisaur> Hi Tony, Thanks for the patch. I'd thought about the 4GB limit in regard to image size but totally forgot about casper-rw. I'm surprised to see it manifest as filesystem corruption without warning though - I'd expect to see an error during the USB stick creation. Let me know if it fixes the issues and I'll patch the package. Cheers, TIM On Fri, 2014-02-28 at 12:07 +0000, Tony Travis wrote: > Hi, Tim. > > I've had problems with filesystem corruption on USB-sticks created from > your 7.0.9 and 7.1.0 Bio-Linux iso images. At first, I thought it was > because I used an old USB-stick, but when I did a r/w test of the raw > device it showed no errors. However, when I tried to use the 'portable' > VirtualBox to 'virtualise' the 7.1.0 stick it complained about my USB > "casper-rw" being larger than 4GiB, which is the maximum file size on a > FAT32 partition - That made me wonder if the filesystem corruption was > caused by "casper-rw" being larger than 4GiB on an 8GiB USB-stick? > > The maximum 'legal' file size for FAT 32 is: > > 2^32 - 1 = 4294967296 -1 bytes = 4GiB - 1 byte > > On my 8GiB sticks, "bio-linux-usb-maker" creates a "casper-rw" > 4GiB. > > This patch limits the size of "casper-rw" to 4095MiB, which is the > largest file size that can be stored 'correctly' on the Bio-Linux > USB-stick FAT32 filesystem. I don't know yet if it will solve the > "casper-rw" corruption problem or not - I'll let you know after I've > done some further testing of USB-sticks made from your 7.1.0 iso. > > Bye, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > The University of Aberdeen is a charity registered in Scotland, No SC013683. -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705