<div dir="ltr"><div><div><div>Hi Tim, <br><br></div>Thank you for sharing this command:<br><br>
wget -qO- <a href="http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh" target="_blank">http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh</a> | env UNPACK_ONLY=1 sh<br><br></div>Now I can finally see what you are doing in file "upgrade_to_8.sh" to transform Ubuntu 14.04 LTS into Biolinux 8.<br><br></div><div>I recently upgraded my system to Ubuntu 15.04 Wily Werewolf (Kernel 4.1rc2) and even after that most of the packages from Biolinux 8 repositories are still working pretty well. I think there is a conflict between the old mate packages from Biolinux in launchpad and the fresh new mate packages from the official Ubuntu repositories. Keep up the good work!<br></div><div><br></div><div>Interesting to see the packages in pseudo_orphans.txt as well!<br><br></div><div>Here are a two bugs I'm receiving while running your script: <br><br><b>This one, probably because of the change from upstart to systemd:</b><br><br>initctl: Unable to connect to Upstart: Failed to connect to socket /com/ubuntu/upstart: Connection refused<br>insserv: warning: script 'galaxy' missing LSB tags and overrides<br>insserv: Default-Start undefined, assuming empty start runlevel(s) for script `galaxy'<br>insserv: Default-Stop undefined, assuming empty stop runlevel(s) for script `galaxy'<br><br><b>And this second one:</b><br><br>E: Unable to locate package bio-linux-jalview<br>Not all packages installed properly - exiting.<br><br></div><div>I believe it's something related with the package "jalview" from biolinux repo. I could install this package from Ubuntu sources without a problem:<br><br> <a href="http://archive.ubuntu.com/ubuntu/">http://archive.ubuntu.com/ubuntu/</a> wily/universe jalview all 2.7.dfsg-4 [3.382 kB]<br><br></div><div><b>Now I have a question, after changing the name of the package in file "bl_master_package_list.txt" from </b><b>bio-linux-jalview to </b><b>jalview, how I could "pack" everything again to the file <a href="http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh" target="_blank">upgrade8.sh</a> or in which order I should execute your scripts bl_install_master_list.sh, pick_cran_mirror.py and upgrade_to_8.sh in order to finally complete the upgrade to Biolinux 8 ?<br></b></div><div><br>I believe I could help this project by packaging some new
software to add to the biolinux repositories or even trying to upgrade a
package from python2 to python3.<br><br>Let me know how I could help. :)<br><div><br></div>Kind Regards,<br><br><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr">_____________________________________________<br><br>Raony Guimarães Corrêa Do Carmo Lisboa Cardenas<br>PhD Student in Bioinformatics<br><br>email: <a href="mailto:raonyguimaraes@gmail.com" target="_blank">raonyguimaraes@gmail.com</a><br>skype/gtalk: raonyguimaraes<br>phone: +55 31 93404152<br><div><br></div><div>Laboratory of Clinical Genomics<br>UFMG School of Medicine</div><div>Federal University of Minas Gerais - UFMG<br>Av. Prof. Alfredo Balena, 190, Sala 321<br>Belo Horizonte, Brazil 30130-100<br>_____________________________________________</div></div></div></div>
<br><div class="gmail_quote">On Wed, May 13, 2015 at 11:24 AM, Simon <span dir="ltr"><<a href="mailto:simon@calmblue.net" target="_blank">simon@calmblue.net</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">On 13/05/15 15:14, Tony Travis wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On 13/05/15 15:01, Simon wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Tim, that's brilliant, thanks.<br>
<br>
Script looks good to me, although I think the PPA will be best for our<br>
situation as we're not running a GUI and the less we vary from our<br>
standard server build the better.<br>
</blockquote>
Hi, Simon.<br>
<br>
I've run Bio-Linux 8 as a terminal server on many servers. You need most<br>
of the Ubuntu 'desktop' installed to run a remote MATE desktop.<br>
<br>
I don't think it's an issue to run a GUI on a server, but you might find<br>
it useful to use the MATE desktop locally if the server graphics<br>
hardware is not up to running Unity.<br>
<br>
The overhead of running a GUI on the server is quite low, especially if<br>
you run the MATE desktop locally. The default remote desktop is MATE.<br>
<br>
HTH,<br>
<br>
Tony.<br>
<br>
</blockquote>
<br></span>
Good to know, thanks, I like MATE. If it turns out that a desktop is required then I'll definitely go down that route.<div class="HOEnZb"><div class="h5"><br>
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