From aleleb at sahfos.ac.uk Thu Sep 4 05:07:42 2014 From: aleleb at sahfos.ac.uk (Alec Colebrook-Clark) Date: Thu, 4 Sep 2014 10:07:42 +0100 Subject: [Bio-Linux] Qiime Message-ID: Hi Tim, I've just had a person mention that the dependencies for qiime 1.8 are throwing out some errors (shown below). qiime > print_qiime_config.py -t System information ================== Platform: linux2 Python version: 2.7.3 (default, Feb 27 2014, 19:58:35) [GCC 4.6.3] Python executable: /usr/bin/python Dependency versions =================== PyCogent version: 1.5.3 NumPy version: 1.6.1 matplotlib version: 1.1.1rc biom-format version: 1.1.2 qcli version: 0.1.0 QIIME library version: 1.8.0 QIIME script version: 1.8.0-1biolinux1 PyNAST version (if installed): 1.2.2 Emperor version: 0.9.3 RDP Classifier version (if installed): rdp_classifier.jar Java version (if installed): 1.7.0_55 QIIME config values =================== blastmat_dir: /usr/share/ncbi/data jobs_to_start: 1 pynast_template_alignment_blastdb: None qiime_scripts_dir: /usr/lib/qiime/bin/ template_alignment_lanemask_fp: /usr/share/qiime/data/lanemask_in_1s_and_0s working_dir: . pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed python_exe_fp: python temp_dir: /tmp blastall_fp: blastall seconds_to_sleep: 60 cluster_jobs_fp: None F..............F....F.......FF...F. ====================================================================== FAIL: test_FastTree_supported_version (__main__.QIIMEDependencyFull) FastTree is in path and version is supported ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 364, in test_FastTree_supported_version % ('.'.join(map(str,acceptable_version)), version_string)) AssertionError: Unsupported FastTree version. 2.1.3 is required, but running 2.1.7. ====================================================================== FAIL: test_gdata_install (__main__.QIIMEDependencyFull) gdata is installed ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 754, in test_gdata_install self.assertTrue(pass_test, "gdata is not installed.") AssertionError: gdata is not installed. ====================================================================== FAIL: test_pplacer_supported_version (__main__.QIIMEDependencyFull) pplacer is in path and version is supported ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 655, in test_pplacer_supported_version "which components of QIIME you plan to use.") AssertionError: pplacer not found. This may or may not be a problem depending on which components of QIIME you plan to use. ====================================================================== FAIL: test_rtax_supported_version (__main__.QIIMEDependencyFull) rtax is in path and version is supported ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 634, in test_rtax_supported_version "which components of QIIME you plan to use.") AssertionError: rtax not found. This may or may not be a problem depending on which components of QIIME you plan to use. ====================================================================== FAIL: test_sourcetracker_installed (__main__.QIIMEDependencyFull) sourcetracker is installed ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 421, in test_sourcetracker_installed ("SOURCETRACKER_PATH is not set. This is " AssertionError: SOURCETRACKER_PATH is not set. This is only important if you plan to use SourceTracker. ====================================================================== FAIL: test_usearch_supported_version (__main__.QIIMEDependencyFull) usearch is in path and version is supported ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 714, in test_usearch_supported_version % ('.'.join(map(str,acceptable_version)), version_string)) AssertionError: Unsupported usearch version. (5, 2, 236).(5, 2, 236) is required, but running USEARCH is not freely redistributable and is thus not included in the default QIIME package. You may obtain a personal copy of the 32-bit program at no charge. To use this feature, please go to: http://www.drive5.com/usearch/download.html Download USEARCH v5.2.236, then: sudo mv usearch* /usr/local/bin/usearch sudo chmod a+x /usr/local/bin/usearch You probably also want to install USEARCH 6.1 as /usr/local/bin/usearch61 . ---------------------------------------------------------------------- Ran 35 tests in 0.221s FAILED (failures=6) As far as I know qiime has always been maintained via the apt-get command. Are other users seeing the same errors? I am particularly puzzled by fasttree. Will qiime 1.8 work with fast tree 2.1.7 but throw the error in the qiimw config test? Thanks Alec -------------- next part -------------- An HTML attachment was scrubbed... URL: From aleleb at sahfos.ac.uk Thu Sep 4 09:38:34 2014 From: aleleb at sahfos.ac.uk (Alec Colebrook-Clark) Date: Thu, 4 Sep 2014 14:38:34 +0100 Subject: [Bio-Linux] Qiime In-Reply-To: References: Message-ID: Hi again! Also what would be the easiest way to install qiime 1.7? Im trying qiime-deploy but having some difficulty. Thanks Alec From: Alec Colebrook-Clark [mailto:aleleb at sahfos.ac.uk] Sent: 04 September 2014 10:08 To: bio-linux at nebclists.nerc.ac.uk Subject: [Bio-Linux] Qiime Hi Tim, I've just had a person mention that the dependencies for qiime 1.8 are throwing out some errors (shown below). qiime > print_qiime_config.py -t System information ================== Platform: linux2 Python version: 2.7.3 (default, Feb 27 2014, 19:58:35) [GCC 4.6.3] Python executable: /usr/bin/python Dependency versions =================== PyCogent version: 1.5.3 NumPy version: 1.6.1 matplotlib version: 1.1.1rc biom-format version: 1.1.2 qcli version: 0.1.0 QIIME library version: 1.8.0 QIIME script version: 1.8.0-1biolinux1 PyNAST version (if installed): 1.2.2 Emperor version: 0.9.3 RDP Classifier version (if installed): rdp_classifier.jar Java version (if installed): 1.7.0_55 QIIME config values =================== blastmat_dir: /usr/share/ncbi/data jobs_to_start: 1 pynast_template_alignment_blastdb: None qiime_scripts_dir: /usr/lib/qiime/bin/ template_alignment_lanemask_fp: /usr/share/qiime/data/lanemask_in_1s_and_0s working_dir: . pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed python_exe_fp: python temp_dir: /tmp blastall_fp: blastall seconds_to_sleep: 60 cluster_jobs_fp: None F..............F....F.......FF...F. ====================================================================== FAIL: test_FastTree_supported_version (__main__.QIIMEDependencyFull) FastTree is in path and version is supported ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 364, in test_FastTree_supported_version % ('.'.join(map(str,acceptable_version)), version_string)) AssertionError: Unsupported FastTree version. 2.1.3 is required, but running 2.1.7. ====================================================================== FAIL: test_gdata_install (__main__.QIIMEDependencyFull) gdata is installed ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 754, in test_gdata_install self.assertTrue(pass_test, "gdata is not installed.") AssertionError: gdata is not installed. ====================================================================== FAIL: test_pplacer_supported_version (__main__.QIIMEDependencyFull) pplacer is in path and version is supported ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 655, in test_pplacer_supported_version "which components of QIIME you plan to use.") AssertionError: pplacer not found. This may or may not be a problem depending on which components of QIIME you plan to use. ====================================================================== FAIL: test_rtax_supported_version (__main__.QIIMEDependencyFull) rtax is in path and version is supported ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 634, in test_rtax_supported_version "which components of QIIME you plan to use.") AssertionError: rtax not found. This may or may not be a problem depending on which components of QIIME you plan to use. ====================================================================== FAIL: test_sourcetracker_installed (__main__.QIIMEDependencyFull) sourcetracker is installed ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 421, in test_sourcetracker_installed ("SOURCETRACKER_PATH is not set. This is " AssertionError: SOURCETRACKER_PATH is not set. This is only important if you plan to use SourceTracker. ====================================================================== FAIL: test_usearch_supported_version (__main__.QIIMEDependencyFull) usearch is in path and version is supported ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/qiime/bin/print_qiime_config.py", line 714, in test_usearch_supported_version % ('.'.join(map(str,acceptable_version)), version_string)) AssertionError: Unsupported usearch version. (5, 2, 236).(5, 2, 236) is required, but running USEARCH is not freely redistributable and is thus not included in the default QIIME package. You may obtain a personal copy of the 32-bit program at no charge. To use this feature, please go to: http://www.drive5.com/usearch/download.html Download USEARCH v5.2.236, then: sudo mv usearch* /usr/local/bin/usearch sudo chmod a+x /usr/local/bin/usearch You probably also want to install USEARCH 6.1 as /usr/local/bin/usearch61 . ---------------------------------------------------------------------- Ran 35 tests in 0.221s FAILED (failures=6) As far as I know qiime has always been maintained via the apt-get command. Are other users seeing the same errors? I am particularly puzzled by fasttree. Will qiime 1.8 work with fast tree 2.1.7 but throw the error in the qiimw config test? Thanks Alec -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Fri Sep 12 10:06:49 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 12 Sep 2014 15:06:49 +0100 Subject: [Bio-Linux] Qiime In-Reply-To: References: Message-ID: <1410530809.6374.83.camel@balisaur> Hi Alec, The QIIME quick self-test you get with "print_qiime_config.py -t" always gives some errors and probably always will because of the way it is set up. I verify the QIIME installation with the more comprehensive regression tests rather than trying to match all the exact software versions they suggest. So yes, QIIME seems to work fine with the newer (actually over a year old) FastTree even though it complains about the version. On the second question - If I knew a truly easy way to install QIIME I wouldn't have gone to all the trouble packaging it for APT! More seriously, I would use their VirtualBox version if possible, because gathering all the old versions of tools needed for the old QIIME will be hard work. Cheers, TIM On Thu, 2014-09-04 at 14:38 +0100, Alec Colebrook-Clark wrote: > Hi again! > > > > Also what would be the easiest way to install qiime 1.7? Im trying > qiime-deploy but having some difficulty. > > > > Thanks > > Alec > > > > From: Alec Colebrook-Clark [mailto:aleleb at sahfos.ac.uk] > Sent: 04 September 2014 10:08 > To: bio-linux at nebclists.nerc.ac.uk > Subject: [Bio-Linux] Qiime > > > > > Hi Tim, > > > > I?ve just had a person mention that the dependencies for qiime 1.8 are > throwing out some errors (shown below). > > > > qiime > print_qiime_config.py -t > > System information > ================== > Platform: linux2 > Python version: 2.7.3 (default, Feb 27 2014, 19:58:35) [GCC 4.6.3] > Python executable: /usr/bin/python > > Dependency versions > =================== > PyCogent version: 1.5.3 > NumPy version: 1.6.1 > matplotlib version: 1.1.1rc > biom-format version: 1.1.2 > qcli version: 0.1.0 > QIIME library version: 1.8.0 > QIIME script version: 1.8.0-1biolinux1 > PyNAST version (if installed): 1.2.2 > Emperor version: 0.9.3 > RDP Classifier version (if installed): rdp_classifier.jar > Java version (if installed): 1.7.0_55 > > QIIME config values > =================== > blastmat_dir: /usr/share/ncbi/data > jobs_to_start: 1 > pynast_template_alignment_blastdb: None > qiime_scripts_dir: /usr/lib/qiime/bin/ > template_alignment_lanemask_fp: /usr/share/qiime/data/lanemask_in_1s_and_0s > working_dir: . > pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed > python_exe_fp: python > temp_dir: /tmp > blastall_fp: blastall > seconds_to_sleep: 60 > cluster_jobs_fp: None > F..............F....F.......FF...F. > ====================================================================== > FAIL: test_FastTree_supported_version (__main__.QIIMEDependencyFull) > FastTree is in path and version is supported > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/qiime/bin/print_qiime_config.py", line 364, in > test_FastTree_supported_version > % ('.'.join(map(str,acceptable_version)), version_string)) > AssertionError: Unsupported FastTree version. 2.1.3 is required, but > running 2.1.7. > > ====================================================================== > FAIL: test_gdata_install (__main__.QIIMEDependencyFull) > gdata is installed > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/qiime/bin/print_qiime_config.py", line 754, in > test_gdata_install > self.assertTrue(pass_test, "gdata is not installed.") > AssertionError: gdata is not installed. > > ====================================================================== > FAIL: test_pplacer_supported_version (__main__.QIIMEDependencyFull) > pplacer is in path and version is supported > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/qiime/bin/print_qiime_config.py", line 655, in > test_pplacer_supported_version > "which components of QIIME you plan to use.") > AssertionError: pplacer not found. This may or may not be a problem > depending on which components of QIIME you plan to use. > > ====================================================================== > FAIL: test_rtax_supported_version (__main__.QIIMEDependencyFull) > rtax is in path and version is supported > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/qiime/bin/print_qiime_config.py", line 634, in > test_rtax_supported_version > "which components of QIIME you plan to use.") > AssertionError: rtax not found. This may or may not be a problem > depending on which components of QIIME you plan to use. > > ====================================================================== > FAIL: test_sourcetracker_installed (__main__.QIIMEDependencyFull) > sourcetracker is installed > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/qiime/bin/print_qiime_config.py", line 421, in > test_sourcetracker_installed > ("SOURCETRACKER_PATH is not set. This is " > AssertionError: SOURCETRACKER_PATH is not set. This is only important > if you plan to use SourceTracker. > > ====================================================================== > FAIL: test_usearch_supported_version (__main__.QIIMEDependencyFull) > usearch is in path and version is supported > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/qiime/bin/print_qiime_config.py", line 714, in > test_usearch_supported_version > % ('.'.join(map(str,acceptable_version)), version_string)) > AssertionError: Unsupported usearch version. (5, 2, 236).(5, 2, 236) > is required, but running > USEARCH is not freely redistributable and is thus not included in the > default QIIME package. > You may obtain a personal copy of the 32-bit program at no charge. > > To use this feature, please go to: > http://www.drive5.com/usearch/download.html > > Download USEARCH v5.2.236, then: > sudo mv usearch* /usr/local/bin/usearch > sudo chmod a+x /usr/local/bin/usearch > > You probably also want to install USEARCH 6.1 > as /usr/local/bin/usearch61 > > . > > ---------------------------------------------------------------------- > Ran 35 tests in 0.221s > > FAILED (failures=6) > > > > > > As far as I know qiime has always been maintained via the apt-get > command. Are other users seeing the same errors? I am particularly > puzzled by fasttree. Will qiime 1.8 work with fast tree 2.1.7 but > throw the error in the qiimw config test? > > > > Thanks > > Alec > > -- 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 tony.travis at abdn.ac.uk Fri Sep 12 16:41:22 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Fri, 12 Sep 2014 21:41:22 +0100 Subject: [Bio-Linux] Qiime In-Reply-To: <1410530809.6374.83.camel@balisaur> References: <1410530809.6374.83.camel@balisaur> Message-ID: <54135A72.1030307@abdn.ac.uk> On 12/09/14 15:06, Tim Booth wrote: > Hi Alec, > > The QIIME quick self-test you get with "print_qiime_config.py -t" always > gives some errors and probably always will because of the way it is set > up. I verify the QIIME installation with the more comprehensive > regression tests rather than trying to match all the exact software > versions they suggest. So yes, QIIME seems to work fine with the newer > (actually over a year old) FastTree even though it complains about the > version. > > On the second question - If I knew a truly easy way to install QIIME I > wouldn't have gone to all the trouble packaging it for APT! More > seriously, I would use their VirtualBox version if possible, because > gathering all the old versions of tools needed for the old QIIME will be > hard work. Hi, Tim. I, sort of, disagree with you about all this because QIIME is validated against specific versions of tools and I installed them all by hand to get it to pass its own tests. That is not, of course, consistent with the spirit of Bio-Linux/Debian-Med packaging of software... QIIME looks like an absolute perfect use-case example for Docker! Instead of using VirtualBox to provide the specific environment that QIIME is validated against, as an alternative we could encapsulate it in a Docker container and run it under Bio-linux (or whatever OS). What do you think? 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. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From aleleb at sahfos.ac.uk Mon Sep 15 02:28:59 2014 From: aleleb at sahfos.ac.uk (Alec Colebrook-Clark) Date: Mon, 15 Sep 2014 07:28:59 +0100 Subject: [Bio-Linux] Qiime In-Reply-To: <54135A72.1030307@abdn.ac.uk> References: <1410530809.6374.83.camel@balisaur> <54135A72.1030307@abdn.ac.uk> Message-ID: Hi Tony and Tim, Thanks for the reply. I appear to and solved the problem by using the QIIME deploy for version 1.8 and then manually installed the USEARCH to get all dependencies to pass the test. It was a headache and I much prefer the APT way of installing it! Thanks Alec -----Original Message----- From: Tony Travis [mailto:tony.travis at abdn.ac.uk] Sent: 12 September 2014 21:41 To: bio-linux at nebclists.nerc.ac.uk Subject: Re: [Bio-Linux] Qiime On 12/09/14 15:06, Tim Booth wrote: > Hi Alec, > > The QIIME quick self-test you get with "print_qiime_config.py -t" > always gives some errors and probably always will because of the way > it is set up. I verify the QIIME installation with the more > comprehensive regression tests rather than trying to match all the > exact software versions they suggest. So yes, QIIME seems to work > fine with the newer (actually over a year old) FastTree even though it > complains about the version. > > On the second question - If I knew a truly easy way to install QIIME I > wouldn't have gone to all the trouble packaging it for APT! More > seriously, I would use their VirtualBox version if possible, because > gathering all the old versions of tools needed for the old QIIME will > be hard work. Hi, Tim. I, sort of, disagree with you about all this because QIIME is validated against specific versions of tools and I installed them all by hand to get it to pass its own tests. That is not, of course, consistent with the spirit of Bio-Linux/Debian-Med packaging of software... QIIME looks like an absolute perfect use-case example for Docker! Instead of using VirtualBox to provide the specific environment that QIIME is validated against, as an alternative we could encapsulate it in a Docker container and run it under Bio-linux (or whatever OS). What do you think? 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. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From tbooth at ceh.ac.uk Thu Sep 25 06:05:59 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 25 Sep 2014 11:05:59 +0100 Subject: [Bio-Linux] Shellshock bug - how dangerous? In-Reply-To: References: <1411549652.20101.14.camel@balisaur> Message-ID: <1411639559.20101.144.camel@balisaur> Hi, This is a really nasty bug, especially if you run CGI scripts on a web server. The good news is that Bio-Linux (being based on Ubuntu) generally uses a mixture of "zsh" and "dash". In most cases where scripts do not explicitly invoke "bash" this will protect CGI scripts from the attack. And most Bio-Linux users are not running public web servers in any case. If you don't know what the above means then you're probably not running anything that will expose you to this bug. But in any case, you should ensure the bash package is updated for peace of mind by running the software updater or "sudo apt-get dist-upgrade" on the command line. I've confirmed on my own system that the latest update 4.3-7ubuntu1.1 is available and patches the issue. tbooth at balisaur[~] apt-cache policy bash bash: Installed: 4.3-7ubuntu1.1 Candidate: 4.3-7ubuntu1.1 ... Cheers, TIM On Wed, 2014-09-24 at 22:43 +0100, Ronny van Aerle wrote: > Should we be worried about the recently discovered Shellshock bug? > http://web.nvd.nist.gov/view/vuln/detail?vulnId=CVE-2014-6271 > http://www.theregister.co.uk/2014/09/24/bash_shell_vuln/ > > > I just want to make sure we're safe! > > > Best wishes, > > Ronny >