- galaxy-dev - lists.galaxyproject.org

Galaxy Conference
by Scott Szakonyi 04 Mar '16

04 Mar '16

Hi all, I know this is not a technical question per se, but this seems my best option for getting better information. I am planning on attending the Galaxy Conference this year. I administrate the Galaxy server for VectorBase (vectorbase.org) but I'm a computer scientist, not a bioinformatics specialist. I'm uncertain what would be the most informative things for me to attend... for instance, I see there is a training day 1 and 2, but there's no real description on the site of what those are. If someone could offer some guidance, I would be most appreciative. Also, would the conference days be useful for someone in my position? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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Python 2.7 six egg fetching issue
by Yves Gagnon 04 Mar '16

04 Mar '16

Hi everyone, When I try to run galaxy using python 2.7 I get this error message while fetching eggs. Under python 2.6 I do not have that issue: DistributionNotFound: six==1.9.0 The galaxy release I use is still 15.07. Is there any fix for that other than building the egg myself, or maybe newer release do not have that issue? Thanks in advance! Yves Gagnon

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Problems with planemo functional tests
by Léo Biscassi 04 Mar '16

04 Mar '16

Hi Folks, I tried follow this tutorial [1], but I have problems in execute the command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for perform functional tests, any suggestion? Bellow some images about this problem: [image: imagem1.jpg] *Figure 1: *Command [image: imagem2.jpg] *Figure 2:* Error [image: imagem3.jpg] *Figure 3: *Galaxy Path Planemo's version is 0.23.0. [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html P.S: The command is utilized for same tool presented in tutorial. Att. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi

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error loading files into galaxy
by Hakeem Almabrazi 04 Mar '16

04 Mar '16

Hi, I started getting the following error whenever I try to load a file into Galaxy local. Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 8, in <module> from galaxy import eggs ImportError: cannot import name eggs I will appreciate if someone can tell me what could happen to cause such issue and how to resolve it. Regards,

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playbook download error
by William Ge 03 Mar '16

03 Mar '16

Hi, all, I tried to download the playbook for automatic installation of Galaxy tools, but encountered the following error: [galaxy@Pegasus galaxy]$ git clone --recursive git@github.com:afgane/galaxy-tools-playbook.git Initialized empty Git repository in /home/galaxy/galaxy/galaxy-tools-playbook/.git/ Permission denied (publickey). fatal: The remote end hung up unexpectedly Is this repository still open to public download? I'm new and not quite familiar with the playbook application. Any step by step guide will be helpful. Thanks, Bill

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nginx data upload request never reaches /api/tools
by Preussner, Jens 03 Mar '16

03 Mar '16

Hi all, I set up the data upload using nginx as described in the wiki (https://wiki.galaxyproject.org/Admin/Config/nginxProxy, using the subdirectory /galaxy). The uploaded file also appears inside the uploade_store folder on the galaxy server, but galaxy does not add the file. Investigating the log files, I found the corresponding lines in the nginx.error.log: # Post request is received 2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches "POST", client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122", referrer: http://172.16.12.122/galaxy/ # Upload starts 2016/02/29 12:55:37 [info] 13156#0: *4 started uploading file "boxes.txt" to "/mnt/idrive1/database/tmp/upload_store/0020132707" (field "files_0|file_data", content type "text/plain"), client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122", referrer: http://172.16.12.122/galaxy/ # Upload done, the file is present in the given path 2016/02/29 12:55:37 [info] 13156#0: *4 finished uploading file "boxes.txt" to "/mnt/idrive1/database/tmp/upload_store/0020132707", client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/" # Redirection starts? 2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches "POST", client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/" 2016/02/29 12:55:37 [notice] 13156#0: *4 "nginx_redir=([^&]+)" does not match "", client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/" 2016/02/29 12:55:37 [notice] 13156#0: *4 "" matches "/_upload_done", client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/" # Redirection should be done here 2016/02/29 12:55:37 [notice] 13156#0: *4 rewritten data: "/galaxy/api/tools", args: "", client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/" # ModSecurity seems to block the redirect? 2016/02/29 12:55:37 [info] 13156#0: *4 ModSecurity: invalid "Content-Length" header, client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/" 2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches "GET", client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/" A ModSecurityEnabled off; within the /_upload and /_upload_done of the nginx config did not help. Any idea why the Content-Length header causes problems and is blocked by modSec? Any workaround for ModSec to accept everything that goes from internal to internal? Thanks for your help! Best, Jens

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workflows "show in menu" by default
by Cameron Jack 02 Mar '16

02 Mar '16

Hi all, In the /workflow/configure_menu screen there is an tickbox option for each installed workflow to "show in menu". Is there a way I could enable this by default, or in code via bioblend (couldn't see any hint of this in the docs)? Perhaps I could extend bioblend to do this? Cheers, Cam Cameron Jack Acting Manager & Bioinformatician ANU Bioinformatics Consultancy The Australian National University The John Curtin School of Medical Research Building 131 Garran Road Acton 0200, ACT Ph (office): +61 2 612 51128 Ph (mobile): +61 4 2368 0745 Email: cameron.jack(a)anu.edu.au Group email: abc(a)anu.edu.au

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Galaxy on Azure
by Alex Lenail 02 Mar '16

02 Mar '16

Hello, My name is Alex LeNail and I'm a researcher at MIT. I'm looking to set up a Galaxy server, and our lab has a great deal of Microsoft Azure credits, so we were hoping to deploy Galaxy on there. Where should I start if I wanted to set that up? I haven't really found any resources online with any description of how that might be accomplished. Thanks, --Alex

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Dependencies for sudo scripts/drmaa_external_runner.py ?
by Peter Cock 02 Mar '16

02 Mar '16

Hello all, QUESTION: When submitting jobs to the cluster as the real user, how should sudo scripts/drmaa_external_runner.py be told which Python to use, and how would it activate the venv if needed for the DRMAA dependency? BACKGROUND: We're currently trying Galaxy out on a new CentOS 6 VM, with matching CentOS 6 cluster, where jobs are submitted to SGE via DRMAA and run as the Linux user rather than a generic Galaxy Linux user account. This is documented on the wiki here: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster This all seemed to be working under Galaxy v15.10 (using eggs), but we're now targeting the recently released Galaxy v16.10 (using wheels) instead and have run into problems. https://github.com/galaxyproject/galaxy/issues/1596 Because Galaxy is deprecating support for Python 2.6 (the default bundled with CentOS 6), we're now using a local copy of Python 2.7 (compiled from source) on a shared mount. This mismatch seems to be the root cause of the problem I will now describe. During job submission to SGE, Galaxy will attempt to run a command like this: $ sudo scripts/drmaa_external_runner.py 1005 /mnt/shared/galaxy/galaxy-dist/database/sge/132.jt_json >From the terminal output from ./run.sh we'd see: RuntimeError: External_runjob failed (exit code 1) Child process reported error: Traceback (most recent call last): File "/mnt/shared/galaxy/galaxy-dist/scripts/drmaa_external_runner.py", line 15, in <module> import drmaa ImportError: No module named drmaa Although a drmaa wheel was installed within the Python 2.7 virtual environment under ~/galaxy-dist/.venv Galaxy makes no attempt to activate the venv for scripts/drmaa_external_runner.py We then installed DRMAA under our local copy of Python 2.7, and realised sudo scripts/drmaa_external_runner.py was not even using this copy of Python. Changing the hash bang line was a crude way to solve that (see below). This in turn lead to finding $DRMAA_LIBRARY_PATH and $SGE_ROOT were not set in the sudo environment. Again, you can hack around this by modifying scripts/drmaa_external_runner.py (see below). In our case, I suspect the least invasive change would be to install the DRMAA libraries under the system provided Python 2.6, and let sudo scripts/drmaa_external_runner.py execute that way. We still need to solve why sudo scripts/drmaa_external_runner.py does not see $DRMAA_LIBRARY_PATH and $SGE_ROOT but we have some clues to follow up on that: http://stackoverflow.com/questions/257616/sudo-changes-path-why Peter P.S. See also https://twitter.com/pjacock/status/704335582651162624 -- Here's our workaround diff - lots of hard coded strings, not portable at all but it worked for testing/debugging: $ git diff scripts/drmaa_external_runner.py diff --git a/scripts/drmaa_external_runner.py b/scripts/drmaa_external_runner.py index a1474fe..61d2383 100755 --- a/scripts/drmaa_external_runner.py +++ b/scripts/drmaa_external_runner.py @@ -1,5 +1,6 @@ +#!/mnt/shared/galaxy/apps/python/2.7.11/bin/python +#Was #!/usr/bin/env python - """ Submit a DRMAA job given a user id and a job template file (in JSON format) defining any or all of the following: args, remoteCommand, outputPath, @@ -12,8 +13,15 @@ import os import pwd import sys +# Hack +# print "$DRMAA_LIBRARY_PATH is %s" % os.environ.get('DRMAA_LIBRARY_PATH') +# print "$SGE_ROOT is %s" % os.environ.get('SGE_ROOT') +os.environ['DRMAA_LIBRARY_PATH'] = '/mnt/sge/lib/lx-amd64/libdrmaa.so' +os.environ['SGE_ROOT'] = '/mnt/sge' + import drmaa DRMAA_jobTemplate_attributes = [ 'args', 'remoteCommand', 'outputPath', 'errorPath', 'nativeSpecification', 'workingDirectory', 'jobName', 'email', 'project' ]

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Load tools without service interruption
by Floreline TOUCHARD 02 Mar '16

02 Mar '16

Hi Galaxy team, Is there a way to add a tool without service interruption ? Something like a "sh run.sh --reload" (not "restart") command. I think I saw this information once, but I can't put my hand on it anymore. Thanks in advance ! F.T

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