[galaxy-dev] GeneTrack-Installation - Version?
Hi everybody, we're hosting our own galaxy instance and the next step should bei the integration of GeneTrack. (Not the tool, that is already included, but the browser, which has to be set up on our own, as i could read on the mailing list.) I've been reading all information on http://genetrack.bx.psu.edu and http://atlas.bx.psu.edu/genetrack/docs/genetrack.html - but I do not really get, which is the current, newest version? The only one to download is available at googlecode (1.0.3) and - according to the information on http://genetrack.bx.psu.edu - there is a newer one (2.0) I tried to run the tests for 1.0.3 but some fail - the logs aren't quite clear about the problem, even on Debug-mode. Could you tell me what version to use and which instructions? Are there limits or other dependencies according to the used python-packages? Hoping for help thanks in advance, Steffi ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Importing Historys in other Galaxy instances
Hi everybody, I got another question concerning our own Galaxy instance. We are trying to import Histories from the public Galaxy server via Export to file (in the public-Galaxy-account), saving the export-Link and Import from File in the account on our local system. But the histories never show up there. As I read in some older mails, you need to be logged in the source account - I was, I checked that. Am I correct that it's possible to copy histories between different Galaxy instances at all? (I assume because it's the only case that makes sense to me..) We thought it might depend on some Apache configuration, but didn't figure it out yet. Maybe someone's got some ideas :-) Regards, Steffi ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Importing Historys in other Galaxy instances
Hi Ross, that is exactly what I tried - Export to file and then enter the link into Import from File. But the History never appears in the account on our Galaxy :( It works between different accounts on main, but not from main to our's.. Am 25.10.2011 11:58, schrieb Ross: Hi, Stefanie. I think you might want a URL pointing to an archived history if you want to move your history to a different Galaxy? I imported your test history into my account on main, then I used the 'export to file' option (it might not be optimally named since it really creates an importable archive) - main returned: Exporting History 'imported: Neue History zum Test'. Use this link to download the archive or import it to another Galaxy server: http://main.g2.bx.psu.edu/history/export_archive?id=735329393657ab63 I just successfully imported from that URL to a private Galaxy and it all looks right. On Tue, Oct 25, 2011 at 6:48 PM, Stefanie Ververs stefanie.verv...@fh-stralsund.de wrote: Am 24.10.2011 21:05, schrieb Jeremy Goecks: So - I'm logged in and the link is accessible. (I tried with different accounts on the public server - that works; but not importing to our own instance.) The history must be Accessible via link: Options --Share/Publish -- Make History Accessible via Link Can you share the history with me? Thanks, J. I tried it, following your instructions. And different follow-ups: 1) Pasting the sharing-Link into the Import a History from an Archive field - doesn't work 2) Opening the link being logged in to the account on OUR instance, that means, the target account, but NOT on the source account. - doesn't work - he tries to import the history on the public server (I assume because the message was about this will delete your current history) When I imported histories from one account to another on the public server, I never used Make History Accessible via Link. I just took the export-Link (the one you can download the history as an archive file.) I even tried uploading the file somewhere else. This is my test-History: http://main.g2.bx.psu.edu/u/stef85/h/neue-history-zum-test Steffi ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Importing Historys in other Galaxy instances
Hi Ross, I checked the following: wget link works, I can download the file. It's not saved as Historyname.tar.gz but as export_archive?id=a69ee3e00cb4d02c. Anyway, I can unpack the archive with tar xfvz. hg head: Änderung:5955:949e4f5fa03a Marke: tip Nutzer: Nate Coraor n...@bx.psu.edu Datum: Mon Aug 29 14:42:04 2011 -0400 Zusammenfassung: Missing import in library_contents.py Where can I find the file (I assume?) paster.log? On 25.10.2011 12:19, Ross wrote: Sorry to hear it's not working for you - that link definitely did work to an Australian Galaxy server behind a relatively tight and fussy firewall. Suggestions: check that it's not a local firewall problem - eg try wget http://main.g2.bx.psu.edu/history/export_archive?id=735329393657ab63 or on the same link you're trying to import - it's just an archive. If that works, then maybe check for an old version of the code your Galaxy is running? eg what does: hg head show from the root of the installation that's failing to import? Is there anything interesting in paster.log after you start an import job that never finishes? On Tue, Oct 25, 2011 at 9:02 PM, Stefanie Ververs stefanie.verv...@fh-stralsund.de wrote: Hi Ross, that is exactly what I tried - Export to file and then enter the link into Import from File. But the History never appears in the account on our Galaxy :( It works between different accounts on main, but not from main to our's.. Am 25.10.2011 11:58, schrieb Ross: Hi, Stefanie. I think you might want a URL pointing to an archived history if you want to move your history to a different Galaxy? I imported your test history into my account on main, then I used the 'export to file' option (it might not be optimally named since it really creates an importable archive) - main returned: Exporting History 'imported: Neue History zum Test'. Use this link to download the archive or import it to another Galaxy server: http://main.g2.bx.psu.edu/history/export_archive?id=735329393657ab63 I just successfully imported from that URL to a private Galaxy and it all looks right. On Tue, Oct 25, 2011 at 6:48 PM, Stefanie Ververs stefanie.verv...@fh-stralsund.dewrote: Am 24.10.2011 21:05, schrieb Jeremy Goecks: So - I'm logged in and the link is accessible. (I tried with different accounts on the public server - that works; but not importing to our own instance.) The history must be Accessible via link: Options -- Share/Publish -- Make History Accessible via Link Can you share the history with me? Thanks, J. I tried it, following your instructions. And different follow-ups: 1) Pasting the sharing-Link into the Import a History from an Archive field -doesn't work 2) Opening the link being logged in to the account on OUR instance, that means, the target account, but NOT on the source account. -doesn't work - he tries to import the history on the public server (I assume because the message was about this will delete your current history) When I imported histories from one account to another on the public server, I never used Make History Accessible via Link. I just took the export-Link (the one you can download the history as an archive file.) I even tried uploading the file somewhere else. This is my test-History: http://main.g2.bx.psu.edu/u/stef85/h/neue-history-zum-test Steffi ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Importing Historys in other Galaxy instances
On 26.10.2011 16:13, Jeremy Goecks wrote: Hi Ross, I checked the following: wgetlink works, I can download the file. It's not saved asHistoryname.tar.gz but as export_archive?id=a69ee3e00cb4d02c. Anyway, I can unpack the archive with tar xfvz. hg head: Änderung:5955:949e4f5fa03a Marke: tip Nutzer: Nate Coraorn...@bx.psu.edu Datum: Mon Aug 29 14:42:04 2011 -0400 Zusammenfassung: Missing import in library_contents.py Where can I find the file (I assume?) paster.log? Best place to look for the error is in the job table. Try this query for your database: -- select id, state, command_line, stdout, stderr from job where tool_id='__EXPORT_HISTORY__' order by id desc; -- and look at the stderr column for some information about the problem. Please send us the command line and the stderr for the problematic jobs; this should help us figure out what's going on. Thanks, J. Hi Jeremy, 76 | ok| python /home/cweinberg/Software/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://main.g2.bx.psu.edu/history/export_archive?id=a69ee3e00cb4d02c ./database/tmp/tmpbxuXL2 --url | Error unpacking tar/gz archive: [Errno 2] No such file or directory: './database/tmp/tmpbxuXL2/tmpBn0UbN' open file 'stderr', mode 'w' at 0x7f1c2cc991e0 | Error cleaning up history import job: [Errno 2] No such file or directory: './database/tmp/tmpbxuXL2/history_attrs.txt' This is one of the db entries, the other ones are similar (different tmp-directories). Looks like a problem with the temporary directories.. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] GeneTrack-Installation - Version?
Hi, I sent this message about two weeks ago, but by now there was no response. I try again, maybe now someone who's got some advice notices :-) Regards, Steffi Original Message Subject:GeneTrack-Installation - Version? Date: Thu, 20 Oct 2011 23:21:25 +0200 From: Stefanie Ververs stefanie.verv...@fh-stralsund.de To: galaxy-dev@lists.bx.psu.edu Hi everybody, we're hosting our own galaxy instance and the next step should bei the integration of GeneTrack. (Not the tool, that is already included, but the browser, which has to be set up on our own, as i could read on the mailing list.) I've been reading all information on http://genetrack.bx.psu.edu and http://atlas.bx.psu.edu/genetrack/docs/genetrack.html - but I do not really get, which is the current, newest version? The only one to download is available at googlecode (1.0.3) and - according to the information on http://genetrack.bx.psu.edu - there is a newer one (2.0) I tried to run the tests for 1.0.3 but some fail - the logs aren't quite clear about the problem, even on Debug-mode. Could you tell me what version to use and which instructions? Are there limits or other dependencies according to the used python-packages? Hoping for help thanks in advance, Steffi ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
