- galaxy-dev - lists.galaxyproject.org

galaxy v16.04 drmaa remote user and local upload
by Laure QUINTRIC 20 Apr '16

20 Apr '16

Hi there, I read this thread : http://dev.list.galaxyproject.org/external-chown-script-py-and-the-local-jo… (sorry not to answer in this thread but I'm new to the list). I'm using galaxy 16.04 (and the corrected files should be included as it is merge in 16.04: https://github.com/galaxyproject/galaxy/pull/1688) with remote user drmaa job execution. I set the upload tool to be executed on local runner in job_conf.xml , I kept the external_chown_script set in galaxy.ini and still get the permission denied error while uploading a file. How should it be configured in galaxy.ini and job_conf.xml to upload files locally and other jobs with drmaa with external_chown_script.py only executed for drmaa tools and not for local ones ? Do you have a working example ? Thanks a lot. Laure

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remote user CAS invalide session
by Laure QUINTRIC 20 Apr '16

20 Apr '16

Hi galaxy users, I just installed version 16.04 of galaxy. I can connect to galaxy with remote user through CAS authentification but my session is invalidated, I get this message in the history : An error occurred while getting updates from the server. Please contact a Galaxy administrator if the problem persists. Details <javascript:void(0)> In paster.log, I can see this : galaxy.web.framework.webapp WARNING 2016-04-18 17:37:47,308 User logged in as 'toto(a)company.fr' externally, but has a cookie as 'toto' invalidating session and just after I can see : galaxy.web.framework.webapp WARNING 2016-04-18 17:37:48,018 User logged in as 'toto' externally, but has a cookie as 'toto(a)company.fr' invalidating session It seems that variables remote_user_email and galaxy_session.user.email ( in galaxy/lib/web/framework/webapp.py) are set to login@maildomain and then set to login only... so the user login is not always the user email address. In the config/galaxy.ini I set remote_user_maildomain = company.fr remote_user_header = HTTP_CAS_UID Can you tell me how to go through this ? I did not have this problem in v16.01. Best regards

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Question: Cannot start local Galaxy after upgrade to v16.01
by D K 19 Apr '16

19 Apr '16

Hi Galaxy Devs, I posted this question on biostars but didn't get an answer so I'll try here: I just tried upgrading my local instance of Galaxy from 15.10 to 16.01. When I start it up I get an error. Does anyone have any suggestions? galaxy@galaxy galaxy$ sh run.sh Activating virtualenv at .venv DEPRECATION: Python 2.6 is no longer supported by the Python core team, please upgrade your Python. A future version of pip will drop support for Python 2.6 Ignoring indexes: https://pypi.python.org/simple /opt/galaxy/.venv/lib/python2.6/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. SNIMissingWarning /opt/galaxy/.venv/lib/python2.6/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwar…. InsecurePlatformWarning Requirement already up-to-date: pip==8.0.2+gx2 in ./.venv/lib/python2.6/site-packages DEPRECATION: Python 2.6 is no longer supported by the Python core team, please upgrade your Python. A future version of pip will drop support for Python 2.6 Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 37)) Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 42)) Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 46)) Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 47)) Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 52)) Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 53)) Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 57)) Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 58)) Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 69)) Requirement already satisfied (use --upgrade to upgrade): importlib in ./.venv/lib/python2.6/site-packages (from kombu==3.0.30->-r requirements.txt (line 40)) Requirement already satisfied (use --upgrade to upgrade): ordereddict in ./.venv/lib/python2.6/site-packages (from kombu==3.0.30->-r requirements.txt (line 40)) You are using pip version 8.0.2+gx2, however version 8.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. DEPRECATION: Python 2.6 is no longer supported by the Python core team, please upgrade your Python. A future version of pip will drop support for Python 2.6 Requirement already satisfied (use --upgrade to upgrade): psycopg2==2.6.1 in ./.venv/lib/python2.6/site-packages (from -r /dev/stdin (line 1)) Requirement already satisfied (use --upgrade to upgrade): importlib==1.0.3 in ./.venv/lib/python2.6/site-packages (from -r /dev/stdin (line 2)) Requirement already satisfied (use --upgrade to upgrade): ordereddict==1.1 in ./.venv/lib/python2.6/site-packages (from -r /dev/stdin (line 3)) Requirement already satisfied (use --upgrade to upgrade): drmaa in ./.venv/lib/python2.6/site-packages (from -r /dev/stdin (line 4)) You are using pip version 8.0.2+gx2, however version 8.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Unsetting $PYTHONPATH Activating virtualenv at .venv Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke exit_code = runner.run(args) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 223, in run result = self.command() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 637, in command server = loadserver(server_spec, name=server_name, relative_to=base, global_conf=vars) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 303, in loadserver return loadobj(SERVER, uri, name=name, **kw) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 319, in loadobj global_conf=global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext global_conf=global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 368, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 502, in get_context section) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 524, in _context_from_use object_type, name=use, global_conf=global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 454, in get_context global_conf=global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext global_conf=global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 376, in _loadegg return loader.get_context(object_type, name, global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 668, in get_context object_type, name=name) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 688, in find_egg_entry_point pkg_resources.require(self.spec) File "/opt/galaxy/lib/pkg_resources.py", line 666, in require needed = self.resolve(parse_requirements(requirements)) File "/opt/galaxy/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: Paste

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Re: [galaxy-dev] Question: Cannot start local Galaxy after upgrade to v16.01
by Scott Szakonyi 19 Apr '16

19 Apr '16

Hi Daniel, I'm a relative novice at Galaxy administration, but at first blush it looks like you're missing (or the Galaxy user doesn't have permissions on) the paste process. You can try a GIT status or diff to see if something just didn't download right. Otherwise, check to make sure that your entire galaxy install directory is owned by the Galaxy user and the group that the Galaxy user belongs to. Hope this helps! pkg_resources.DistributionNotFound: Paste -- 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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novice galaxy user needs help retrieving MIA history
by ryan stueve 19 Apr '16

19 Apr '16

Greetings, I am a novice Galaxy user. I was getting along perfectly this morning (made some mistakes, deleted some steps) and got to alignment steps in my RNAseq analysis. Went to some afternoon meetings, returned & logged back in- MY HISTORY WAS EMPTY! can you advise? Instance: MAIN/publicUsername/email: jnkaccnt1(a)outlook.comHistory name: something like "LUAD RNA-seq"; definitely had "LUAD" in title also, here is one of the steps/filenames that should be in history (I downloaded before meeting):"Galaxy240-[H1648_TopHat_on_data_164_and_data_163__accepted_hits].bam" any help sincerely appreciated

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Issue with GATK in workflow
by Scott Szakonyi 18 Apr '16

18 Apr '16

Hello all, We have indexed a genome using the appropriate data manager, for GATK, and our reference is showing up and working for individual walkers in GATK 2.8. When designing a workflow, however, the reference genome is not appearing as an option for many walkers, including indel realigner and realigner target creator. It is appearing for haplotype caller. Again outside of the workflow environment the indexed references show up for all walkers. Any thoughts on this issue? 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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Order of element in datasetcollection "List"
by julie dubois 18 Apr '16

18 Apr '16

Hi all, I've created a tool which takes a collection List as input. This tool iterate on this collection with a "for" loop. I'd like to know the order of my datasets in this collection for the next treatment in my tools. For example, when I take dataset number 1 and number 2 and number 3 to create my collection. When I iterate on it : what is the first element? the number 1 or the number 3. I ask it because I've seen that when a tool works on a dataset collection, the first job in the history (number of dataset in history is the lowest) ran on dataset number3 and not on dataset number 1 as I expected ! Thanks in advance. Julie Chevalier

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Allow users to see the job queue?
by Raymond Wan 15 Apr '16

15 Apr '16

Dear all, I know Galaxy is independent of the underlying queuing system but is it possible to display the status of the queue to users via the Galaxy interface? I understand that the jobs are submitted under the name of the owner of the Galaxy process. And that there is a way to fix this [1], but I think I'm fine with leaving it as-is. I guess it would be nice if users can see how long the queue is. The naive way that I'm thinking about is to have a cronjob that runs "squeue" (we are using SLURM) periodically. Its output is cleaned up by a script and a "static" HTML file is generated for Galaxy to display. I don't know if there is a more sensible way that fits within the framework of Galaxy. Is this approach acceptable or is there a better / easier way that I've completely missed? Thank you! Ray [1] https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_…

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Data removal after ftp import.
by Zuzanna K. Filutowska 15 Apr '16

15 Apr '16

Dear All, is there any option to not remove files that has been imported to Galaxy from FTP directory and to not remove files that haven't been imported since 3 days? -- Regards, -- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating

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Tool shed tools, manual dep installation
by David Trudgian 15 Apr '16

15 Apr '16

Hi All, I'm currently caught between the requests of our Galaxy users to install things from main tool-shed, and our information security dept's concerns r.e. the automated installation of tool-deps on our systems. Due to restrictive web access policies for servers here our galaxy server can't access SourceForge, where many tool-dep downloads are. A request to unblock this for a particular tool-dep package led to our infosec justifiably raising concerns r.e. a tool-dep package that is quite out of date (details sent off list previously). We're now currently unable to install tool-shed tools that users have requested. The current proposal from our infosec dept is to get all our deps from system repos etc. However the way I'm aware of implementing this for tool-shed tools, which need to run across our cluster, would be something pretty arduous like: * Clone the tool from the upstream toolshed repo * Edit the tool code to remove the package requirements * Identify and install all the requirements on the cluster as system pkgs / environment modules - with attention to versions so things work as expected * Edit the tool code so it knows to load the right environment modules / set right PATH when it runs * Install the tool into our galaxy 'tools' dir , not the 'shed_tools' * Manually add the tool to galaxy's tool_conf.xml.main * Schedule downtime to restart galaxy * Test things out .... or we have to host our own tool shed, import tools we want from upstream, edit out the package requirements, provide the deps ourselves. These have all the headaches of merging things in when upstream shed-tools change. Just wondering if I'm missing anything? I know you can turn off 'handle repository dependencies' when installing a tool, but the tool still defines 'requirements' in its XML file and shows 'Missing repository/tool dependencies' in the Admin. Has anyone had any experience of dealing with this kind of situation? Many thanks! -- David Trudgian Ph.D. Computational Scientist, BioHPC Lyda Hill Department of Bioinformatics UT Southwestern Medical Center Dallas, TX 75390-9039 Tel: (214) 648-4833 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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