Re: [galaxy-dev] ClustalW jobs aren't working
On 06/09/2014 07:33 PM, Malcolm Tobias wrote: All, I apologize for an off-topic question, by my update failed: [galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg pull -u | tee hg.pull.out ... added 3716 changesets with 9929 changes to 2124 files (+46 heads) ... merging lib/galaxy/app.py merging lib/galaxy/app.py failed! warning: conflicts during merge. merging lib/galaxy/model/__init__.py merging lib/galaxy/model/__init__.py failed! warning: conflicts during merge. merging lib/galaxy/model/mapping.py merging lib/galaxy/model/mapping.py failed! merging tool-data/shared/ucsc/ucsc_build_sites.txt and tool-data/shared/ucsc/ucsc_build_sites.txt.sample to tool-data/shared/ucsc/ucsc_build_sites.txt.sample 1528 files updated, 1 files merged, 1289 files removed, 3 files unresolved use 'hg resolve' to retry unresolved file merges resolve apparently can't fix this issue: [galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg resolve --all merging lib/galaxy/app.py warning: conflicts during merge. merging lib/galaxy/app.py failed! merging lib/galaxy/model/__init__.py warning: conflicts during merge. merging lib/galaxy/model/__init__.py failed! merging lib/galaxy/model/mapping.py warning: conflicts during merge. merging lib/galaxy/model/mapping.py failed! What's the recommended way to fix this? Depending on your local customization, it is not unusual to get unresolved files. Open the files in an editor and complete the merge manually. Regards, Hans-Rudolf Thanks! Malcolm On Monday 09 June 2014 10:47:04 Malcolm Tobias wrote: Ross, Thanks for the response. My instance of Galaxy is indeed ancient: [galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg tip changeset: 10003:b4a373d86c51 tag: tip parent: 10001:471484ff8be6 user: greg date: Wed Jun 12 11:48:09 2013 -0400 summary: Add targets to Repository Actions menu items. Previous attempts at updating have been pretty painful. I'll give it a shot and let you know whether or not this fixes the problem. Cheers, Malcolm On Friday 06 June 2014 18:30:01 Ross wrote: Hi Malcolm, That error makes me think you might be running an outdated version of galaxy code - the toolshed code has undergone extensive revision over the last few months? I just tested that repository on a freshly updated galaxy-central clone and it installed without drama, so I wonder what: hg tip shows? I just tested using : (vgalaxy)rlazarus@rlazarus-UX31A:~/galaxy$ hg tip changeset: 13756:84a00e4f7d06 tag: tip user:Dannon Baker dannonba...@me.com date:Fri Jun 06 17:12:30 2014 -0400 summary: Clarify language in DeleteIntermediateDataset PJA. If your clone is not up to date, I'd recommend completely removing the failed installation (through the admin menu - check the box for complete removal), shut down galaxy, backup your database, do the usual hg pull -u dance and any necessary database upgrade steps then try a clean install? Thanks for reporting this - if it persists on recent Galaxy code we'll need to do some deeper investigation. On Fri, Jun 6, 2014 at 11:32 PM, Malcolm Tobias mtob...@wustl.edu wrote: Ross, Thanks for the reply! Unfortunately I am the local Galaxy admin ;-) I had tried installing the clustalw tool from the toolshed, but that failed with an error (more on that later). I disabled the local tool: [galaxy@login002 galaxy-dist]$ diff tool_conf.xml tool_conf.xml.bkup 226a227,229 section name=Multiple Alignments id=clustal tool file=rgenetics/rgClustalw.xml / /section bounced galaxy in case that's necessary, then retried installing from the toolshed. Shortly after clicking install, I get this message: Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. The logs appear to be complaining about 'prior_installation_required' which I'm assuming means the package_clustalw_2_1 dependency. I was able to install that, and I can verify by looking at the local toolshed: [galaxy@login002 ~]$ ls galaxy-toolshed/toolshed.g2.bx.psu.edu/repos/devteam/ bowtie_wrappers package_clustalw_2_1 package_vcftools_0_1_11 bwa_wrappers package_fastx_toolkit_0_0_13 Again, I'll post the logs from when the install fails in case that helps. Any suggestions are much appreciated. Cheers, Malcolm 10.28.56.101 - - [06/Jun/2014:08:20:38 -0500] GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=0e5d027cf47ecae0changeset_revisions=7cc64024fe92 HTTP/1.1 500 -
[galaxy-dev] installing htseq-count from tool-shed
Hi, I am trying to install the tool htseq-count from the tool-shed. I had a problem in the first installation so I uninstalled the tool and all its dependencies (numpy, samtools 0.1.19 and pysam) from the 'manage installed tool shed repositories) and installed it again but then I get installation status 'Installed, missing tool dependencies' for htseq-count. When running this tool I get the error Fatal error: The HTSeq python package is not properly installed, contact Galaxy administrators The path set in universe_wsgi.ini: tool_dependency_dir = /home/galaxy/galaxy-dist/tool_deps in the installation log htseq/0.6.1/lparsons/htseq_count/d5edaf8dc974/INSTALLATION.log I get the error: Setup script for HTSeq: Failed to import 'numpy'. Please install numpy and then try again to install HTSeq. I reinstalled numpy but that did not help. How should I continue? Thanks, Karen ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] installing htseq-count from tool-shed
Hi Karen, Sorry your having trouble with installing the tool. It seems that the somehow, the numpy dependency didn't install properly or isn't being found during the HTSeq install. Is there any other info in the log to indicate an issue with installing Numpy? Also, what OS are you running Galaxy on? Lance On June 10, 2014 4:04:13 AM EDT, Karen Chait kch...@techunix.technion.ac.il wrote: Hi, I am trying to install the tool htseq-count from the tool-shed. I had a problem in the first installation so I uninstalled the tool and all its dependencies (numpy, samtools 0.1.19 and pysam) from the 'manage installed tool shed repositories) and installed it again but then I get installation status 'Installed, missing tool dependencies' for htseq-count. When running this tool I get the error Fatal error: The HTSeq python package is not properly installed, contact Galaxy administrators The path set in universe_wsgi.ini: tool_dependency_dir = /home/galaxy/galaxy-dist/tool_deps in the installation log htseq/0.6.1/lparsons/htseq_count/d5edaf8dc974/INSTALLATION.log I get the error: Setup script for HTSeq: Failed to import 'numpy'. Please install numpy and then try again to install HTSeq. I reinstalled numpy but that did not help. How should I continue? Thanks, Karen ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] SAM/BAM To Counts dataset generation errors
When trying SAM/BAM to Counts I get the following error message: pysam not installed; please install it But a) pysam was not in this tool dependencies; b) pysam/0.7.7 is already installe -- [image: Israel Bravo on about.me] Israel Bravo about.me/bravobih http://about.me/bravobih ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Missing navigation pane
I installed a local instance of galaxy approximately a month ago (build 2014.04.14). I was having an issue with the Data Manager to fetch reference genomes and after checking to see if there was a newer version of galaxy, I decided to update and see if that fixed my problem. I ran hg pull and then hg update latest_2014.06.02. I tried to rerun galaxy but was instructed to run manage_db.sh so I did (sh manage_db.sh upgrade). When I ran galaxy after all this, it started but when opened in a web browser, the navagation pane at the top is missing (i.e. Analyze Data, Workflows, User, etc). There is a blue bar but nothing is on it. How do I get the missing navigation pane back? I can't do a lot of things without it (i.e. check help or change user settings). I can still get to the administrator section but only by appending /admin to the url. I need to know how to fix the new version or how to succesfully revert to a previous version without anything else breaking. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing navigation pane
Hey Stephen, Can you look in the server logs to see if there are any errors being reported? Or if there are any javascript errors in the browser window? You may also want to try clearing your browser cache. -Dannon On Tue, Jun 10, 2014 at 1:54 AM, Stephen E sedwards...@hotmail.com wrote: I installed a local instance of galaxy approximately a month ago (build 2014.04.14). I was having an issue with the Data Manager to fetch reference genomes and after checking to see if there was a newer version of galaxy, I decided to update and see if that fixed my problem. I ran hg pull and then hg update latest_2014.06.02. I tried to rerun galaxy but was instructed to run manage_db.sh so I did (sh manage_db.sh upgrade). When I ran galaxy after all this, it started but when opened in a web browser, the navagation pane at the top is missing (i.e. Analyze Data, Workflows, User, etc). There is a blue bar but nothing is on it. How do I get the missing navigation pane back? I can't do a lot of things without it (i.e. check help or change user settings). I can still get to the administrator section but only by appending /admin to the url. I need to know how to fix the new version or how to succesfully revert to a previous version without anything else breaking. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems
Hello All, Thanks for the well laid out e-mails and great discussion. I think John-Paul's comment about the code growing up organically is probably exactly right. (A link below has some details from Nate about this). So late last night I opened a sprawling pull request that cleaned up a lot of stuff in upload.py and then realized it was a little bit incorrect and wouldn't actually help any of you until you were able to upgrade to the August 2014 release :) so I declined. I have reworked a relatively small patch to fix the immediate problem of the consistency tmpfile consistency as it relates to shutil.move. John-Paul Robinson, can you apply it directly and see if it fixes your problems? https://bitbucket.org/jmchilton/galaxy-central-fork-1/commits/dc706d78d9b21a1175199fd9201fe9781d48ffb5/raw If it does, the devteam will get this merged and I will continue with the upload.py improvements that were inspired by this discussion (see https://bitbucket.org/galaxy/galaxy-central/pull-request/408 for more details). -John On Mon, Jun 9, 2014 at 2:50 PM, John-Paul Robinson j...@uab.edu wrote: We've considered the sudo solution, but it opens the window to other bugs giving galaxy the power to change ownership of other files in our shared user cluster environment. We could isolate the power to a script but then we still need to monitor this code closely. We'd prefer not to introduce that requirement. I didn't have the time to trace this down either. ;) I just got tired of this issue and the inconsistent failures causing confusion in our community. I hope your insight into the logic drift over time is accurate and can be corrected. The upload code looks like it's gone through a whole lot of organic growth. :/ Looking forward to additional comments from the dev team. ~jpr On 06/09/2014 03:30 PM, Kandalaft, Iyad wrote: Hi JPR, I had the same questions while trying to figure out a fool-proof way to allow users to import files into galaxy on our Cluster. I couldn't exactly figure out, nor did I have the time to really review, why the galaxy code did these steps and why that shutil.move failed. I opted to simply insert code in upload.py to sudo chown/chmod the files as an easier hack to this problem. There are pros and cons to using the tmp var from the env, and it will depend on your intentions/infrastructure. I think the ideology was that the Galaxy folder was supposed to be shared across all nodes in a cluster, and they opted to use the TMP path within the galaxy folder. Overtime, the code probably partially diverged from that notion, which caused this dilemma. I believe that the best fix is to make the underlying code simply copy the files into the environment-provided temp, which is configurable in galaxy's universe_wsgi.ini, and assume ownership from the get-go. This code of copying and/or moving in discrete steps creates unnecessary complexity. Regards, Iyad -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John-Paul Robinson Sent: Monday, June 09, 2014 3:08 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems There appears to be some inconsistent use of tempfile.mkstemp() within upload.py that causes problems when users import data files to galaxy from a cluster directory via the upload process and import/temp/dataset directories are on different file systems. The issue manifests when Galaxy's job directory, dataset directory and import directory are on different file systems (common for cluster environments) in conjunction with a configuration where users can copy their data files directly to the import directory from which Galaxy selects data sets to upload (as opposed to using an FTP gateway). While allowing users to copy files to an import directory rather than using the FTP gateway may not be that common, we use this configuration locally to help build a more seamless interface with our local collection of HPC resources. Users can be logged into their cluster account and move data into galaxy with a file copy command rather than having to use FTP. This configuration has worked well in our environment as long as the correct ownership configuration existed on the import directory and as long as the import directory, job temporary directory, and galaxy data set directory were all on the same file system. We now have our galaxy dataset directory on a different file system and are seeing inconsistent behavior during the upload.py runs depending on if the data is ordinary text, BAM files, or gzipped data. A subset of uploads will fail because of the way temporary files are created by Galaxy to facilitate the import and any associated conversion processes of different file types. During the import, 1) Galaxy will copy the original file
[galaxy-dev] Tracking tool execution time?
Is there a way to look at how long a galaxy tool takes to run? Jim ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Toolshed update list?
Is there any way to access a list of repository updates in a toolshed, perhaps as an RSS feed? Alternatively, is this data available internally and it just requires writing a route to handle that query? As of now when I log into my toolshed I'm faced with a page of meaningless hashes and version numbers which I cannot mentally track for updates across multiple days/projects. Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 tel:4046922048 e...@tamu.edu mailto:e...@tamu.edu ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy updated botched?
Hi Everyone, This is follow-up information/questions to the issue I ran into with the galaxy June 2nd, 2014 update. I hope to receive feedback on how to proceed. Background: - Running Galaxy (DB Schema 118) with a MySQL 5.5 back-end - When updating galaxy to the june 2nd release, the v120 DB schema has referential integrity constraints, which produced errors during the upgrade. - Completed two galaxy updates in the past 4 months without encountering this before (schema changes included) Discussion: In the past, referential integrity in the DB schema was never an issue. I checked backups and the current database to find that the database tables are using the MyISAM engine. MyISAM = no referential integrity support, no transactions. I reviewed galaxy's SQLAlchemy templates and determined that mysql_engine='InnoDB' isn't set on tables. This explains why all tables were created with the MyISAM engine. If the mysql_engine is not innodb, SQL Alchemy is supposed to drop any referential integrity constraints defined in the schema. What I don't understand is why SQL Alchemy is no longer ignoring the referential integrity constraints. Going forward, can anyone propose how I can salvage the database or continue ignoring referential integrity for now? Assuming that my limited understanding of SQLAlchemy holds water, I was looking at fixing the galaxy code base but I need some clarification on the DB schema versioning. Do I edit schema v1 and add the appropriate table args to make every table an innodb engine table or do I add a new schema and modify all tables to use the innodb engine? Alternatively, I can use DDL events def after_create(target, connection, **kw): connection.execute(ALTER TABLE %s ENGINE=InnoDB; (target.name, target.name)) Thank you for your help. Regards, Iyad Kandalaft Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: iyad.kandal...@agr.gc.camailto:iyad.kandal...@agr.gc.ca Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] troubleshooting Galaxy with LSF
Hello, This is largely a repost from the biostar forum following the suggestion there to post here. I'm doing my first steps in setting up a Galaxy server with an LSF job scheduler. Recently LSF started supporting DRMAA again so I decided to give it a go. I have two setups. The one that works is a stand along server (OpenSuse 12.1, python 2.7.2, LSF 9.1.2). By works I mean that when I login into Galaxy using a browser and upload a file, a job gets submitted and run and everything seems fine. The second setup does not work (RH 6.4, python 2.6.6, LSF 9.1.2). It's a server running Galaxy which is meant to submit jobs to an LSF cluster. When I similarly pick and download a file I get Job 72266 is submitted to queue short. ./run.sh: line 79: 99087 Segmentation fault python ./scripts/paster.py serve universe_wsgi.ini $@ For the moment, I'm not bothered with the full server setup, I'm just testing whether Galaxy works with LSF and therefore run ./run.sh as a user. The job configuration job_conf.xml is identical in both cases: ?xml version=1.0? job_conf plugins plugin id=lsf type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner param id=drmaa_library_path/opt/gridware/lsf/9.1/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so/param /plugin /plugins handlers handler id=main/ /handlers destinations default=lsf_default destination id=lsf_default runner=lsf param id=nativeSpecification-W 24:00/param /destination /destinations /job_conf run.sh is only changed to allow remote access. Most recently I tried replacing python with 2.7.5 to no avail. Still the same kind of error. I also updated Galaxy. Any hints would be much appreciated. Thank you ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] troubleshooting Galaxy with LSF
This is just a guess, which may help you troubleshoot. It could be a that python is reaching a stack limit: run ulimit -s and set it to a higher value if required I’m completely guessing here but is it possible that the DRMAA is missing a linked library on the redhat system – check with ldd? Regards, Iyad Kandalaft Iyad Kandalaft Microbial Biodiversity Bioinformatics Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada 960 Carling Ave.| 960 Ave. Carling Ottawa, ON| Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel iyad.kandal...@agr.gc.ca Telephone | Téléphone 613-759-1228 Facsimile | Télécopieur 613-759-1701 Teletypewriter | Téléimprimeur 613-773-2600 Government of Canada | Gouvernement du Canada From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of I Kozin Sent: Tuesday, June 10, 2014 12:42 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] troubleshooting Galaxy with LSF Hello, This is largely a repost from the biostar forum following the suggestion there to post here. I'm doing my first steps in setting up a Galaxy server with an LSF job scheduler. Recently LSF started supporting DRMAA again so I decided to give it a go. I have two setups. The one that works is a stand along server (OpenSuse 12.1, python 2.7.2, LSF 9.1.2). By works I mean that when I login into Galaxy using a browser and upload a file, a job gets submitted and run and everything seems fine. The second setup does not work (RH 6.4, python 2.6.6, LSF 9.1.2). It's a server running Galaxy which is meant to submit jobs to an LSF cluster. When I similarly pick and download a file I get Job 72266 is submitted to queue short. ./run.sh: line 79: 99087 Segmentation fault python ./scripts/paster.py serve universe_wsgi.ini $@ For the moment, I'm not bothered with the full server setup, I'm just testing whether Galaxy works with LSF and therefore run ./run.sh as a user. The job configuration job_conf.xml is identical in both cases: ?xml version=1.0? job_conf plugins plugin id=lsf type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner param id=drmaa_library_path/opt/gridware/lsf/9.1/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so/param /plugin /plugins handlers handler id=main/ /handlers destinations default=lsf_default destination id=lsf_default runner=lsf param id=nativeSpecification-W 24:00/param /destination /destinations /job_conf run.sh is only changed to allow remote access. Most recently I tried replacing python with 2.7.5 to no avail. Still the same kind of error. I also updated Galaxy. Any hints would be much appreciated. Thank you ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems
Thanks for proposing a patch. We're looking at trying it out on our code base but are at least a few revisions behind and may need to do a little back porting (or catching up). Let me make sure I understand the intention of the patch, though. From the code changes, I trust that the intention is that all temporary files should be created in the Galaxy dataset directory. That is the temp directory path will be the explicitly derived from the output_path that is an argument to upload.py. This is fine. I'm somewhat partial to the environment influencing the TMP dir via an unadorned mkstemp() but I can appreciate having a definitive output_path specified on the call to upload.py. One issue that will affect us slightly (but probably not others) is that we currently have our dataset path on a glusterfs volume which doesn't support ACLs. This means we won't have a way of overriding umask settings that may be in place for the user. If a user with umask 022 writes a file to their import dir, the permissions will at best be read-only for the galaxy processes group owner. This may prevent with the os.rename as well. With a default ACL we could cause the umask to be ignored in favor of a permissive ACL. This is really a local deploy issue but it's worth knowing about. A second question, it looks like the patch only updates convert_newlines and convert_newlines_sep2tabs. The handle_compressed_file and sep2tabs methods in sniff also have bare mkstemp() calls. Do they need modification as well? ~jpr On 06/10/2014 10:49 AM, John Chilton wrote: Hello All, Thanks for the well laid out e-mails and great discussion. I think John-Paul's comment about the code growing up organically is probably exactly right. (A link below has some details from Nate about this). So late last night I opened a sprawling pull request that cleaned up a lot of stuff in upload.py and then realized it was a little bit incorrect and wouldn't actually help any of you until you were able to upgrade to the August 2014 release :) so I declined. I have reworked a relatively small patch to fix the immediate problem of the consistency tmpfile consistency as it relates to shutil.move. John-Paul Robinson, can you apply it directly and see if it fixes your problems? https://bitbucket.org/jmchilton/galaxy-central-fork-1/commits/dc706d78d9b21a1175199fd9201fe9781d48ffb5/raw If it does, the devteam will get this merged and I will continue with the upload.py improvements that were inspired by this discussion (see https://bitbucket.org/galaxy/galaxy-central/pull-request/408 for more details). -John On Mon, Jun 9, 2014 at 2:50 PM, John-Paul Robinson j...@uab.edu wrote: We've considered the sudo solution, but it opens the window to other bugs giving galaxy the power to change ownership of other files in our shared user cluster environment. We could isolate the power to a script but then we still need to monitor this code closely. We'd prefer not to introduce that requirement. I didn't have the time to trace this down either. ;) I just got tired of this issue and the inconsistent failures causing confusion in our community. I hope your insight into the logic drift over time is accurate and can be corrected. The upload code looks like it's gone through a whole lot of organic growth. :/ Looking forward to additional comments from the dev team. ~jpr On 06/09/2014 03:30 PM, Kandalaft, Iyad wrote: Hi JPR, I had the same questions while trying to figure out a fool-proof way to allow users to import files into galaxy on our Cluster. I couldn't exactly figure out, nor did I have the time to really review, why the galaxy code did these steps and why that shutil.move failed. I opted to simply insert code in upload.py to sudo chown/chmod the files as an easier hack to this problem. There are pros and cons to using the tmp var from the env, and it will depend on your intentions/infrastructure. I think the ideology was that the Galaxy folder was supposed to be shared across all nodes in a cluster, and they opted to use the TMP path within the galaxy folder. Overtime, the code probably partially diverged from that notion, which caused this dilemma. I believe that the best fix is to make the underlying code simply copy the files into the environment-provided temp, which is configurable in galaxy's universe_wsgi.ini, and assume ownership from the get-go. This code of copying and/or moving in discrete steps creates unnecessary complexity. Regards, Iyad -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John-Paul Robinson Sent: Monday, June 09, 2014 3:08 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems There appears to be some inconsistent use of tempfile.mkstemp() within upload.py that causes problems when users
Re: [galaxy-dev] inconsistent use of tempfile.mkstemp during upload causes problems
On Tue, Jun 10, 2014 at 1:50 PM, John-Paul Robinson j...@uab.edu wrote: Thanks for proposing a patch. We're looking at trying it out on our code base but are at least a few revisions behind and may need to do a little back porting (or catching up). I think it has been a while since this stuff has been significantly modified - I would guess the patch applies cleanly for last half dozen releases. Let me make sure I understand the intention of the patch, though. From the code changes, I trust that the intention is that all temporary files should be created in the Galaxy dataset directory. That is the temp directory path will be the explicitly derived from the output_path that is an argument to upload.py. The attempt is for all temp files that will just be moved into output_path anyway be created and written out in the same directory as output_path. It is difficult to imagine scenarios where this is not on the same file system as output_path - this means shutil.move should be maximally performant and minimally error prone (agreed?). In general I agree that tools shouldn't really be modifying the TMPDIR - the system configuration should be used and the upload process may still result in some /tmp files - for instance uploading bam files causes some files for samtools stdout and stderr to be written to /tmp. This patch allow them to - because these files will never be moved to the output_path directory. This is fine. I'm somewhat partial to the environment influencing the TMP dir via an unadorned mkstemp() but I can appreciate having a definitive output_path specified on the call to upload.py. Responded to this above. One issue that will affect us slightly (but probably not others) is that we currently have our dataset path on a glusterfs volume which doesn't support ACLs. This means we won't have a way of overriding umask settings that may be in place for the user. If a user with umask 022 writes a file to their import dir, the permissions will at best be read-only for the galaxy processes group owner. This may prevent with the os.rename as well. With a default ACL we could cause the umask to be ignored in favor of a permissive ACL. This is really a local deploy issue but it's worth knowing about. So this expanded version of this pull request that will hopefully be included with the next Galaxy release in July should centralize some of the handling of this and have fewer paths through the code meaning it will be easier to tailor to your local deployment. At that time - if there is more we can do - adding different options, extension points, etc... to further ease your deployment let me know. A second question, it looks like the patch only updates convert_newlines and convert_newlines_sep2tabs. The handle_compressed_file and sep2tabs methods in sniff also have bare mkstemp() calls. Do they need modification as well? Okay - so sep2tabs is used nowhere in Galaxy as far as I can tell. I would like to just delete it at some point. handle_compressed_file is never used during upload.py as far as I can tell - it is for formal data source tools - which should all behave more like normal jobs and normal Galaxy tools - so this is less likely to be a problem. There are some assertions in that last sentence I could be wrong about - and if that method proves problematic let me know and we can deal with it. Thanks again for the e-mail and for pushing Galaxy forward on this, -John ~jpr On 06/10/2014 10:49 AM, John Chilton wrote: Hello All, Thanks for the well laid out e-mails and great discussion. I think John-Paul's comment about the code growing up organically is probably exactly right. (A link below has some details from Nate about this). So late last night I opened a sprawling pull request that cleaned up a lot of stuff in upload.py and then realized it was a little bit incorrect and wouldn't actually help any of you until you were able to upgrade to the August 2014 release :) so I declined. I have reworked a relatively small patch to fix the immediate problem of the consistency tmpfile consistency as it relates to shutil.move. John-Paul Robinson, can you apply it directly and see if it fixes your problems? https://bitbucket.org/jmchilton/galaxy-central-fork-1/commits/dc706d78d9b21a1175199fd9201fe9781d48ffb5/raw If it does, the devteam will get this merged and I will continue with the upload.py improvements that were inspired by this discussion (see https://bitbucket.org/galaxy/galaxy-central/pull-request/408 for more details). -John On Mon, Jun 9, 2014 at 2:50 PM, John-Paul Robinson j...@uab.edu wrote: We've considered the sudo solution, but it opens the window to other bugs giving galaxy the power to change ownership of other files in our shared user cluster environment. We could isolate the power to a script but then we still need to monitor this code closely. We'd prefer not to introduce that requirement. I didn't have the
[galaxy-dev] upload problems
Hi all, I'm working with a problem with user uploaded files. After digging through the logs a bit and running the commands on at a time manually I think I've narrowed it to a permissions problem. This was confirmed by just running galaxy as root and the problem went away ;) -bash-4.1$ PYTHONPATH=/panfs/storage.local/software/galaxy-dist/lib/ -bash-4.1$ python /panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py /panfs/storage.local/software/galaxy-dist//panfs/storage.local/scratch/galaxy-data/tmp/tmpSuHquR /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf 6:/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/6/dataset_6_files:/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/6/galaxy_dataset_6.dat Traceback (most recent call last): File /panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py, line 394, in module __main__() File /panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py, line 369, in __main__ registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] ) File /panfs/storage.local/software/galaxy-dist/lib/galaxy/datatypes/registry.py, line 97, in load_datatypes tree = galaxy.util.parse_xml( config ) File /panfs/storage.local/software/galaxy-dist/lib/galaxy/util/__init__.py, line 154, in parse_xml tree = ElementTree.parse(fname) File build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py, line 859, in parse File build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py, line 576, in parse IOError: [Errno 13] Permission denied: '/panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf' -bash-4.1$ ls -l /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf -rw--- 1 dcshrum dcshrum 317 Jun 10 16:30 /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf It does not look like galaxy is using sudo to run the script. Suggestions to work this out? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] upload problems
You didn't include this context, but I am guessing you are attempting to run jobs as the real user? If not, ignore the rest of the e-mail. I would generally not recommend running the uploads as real user - it is a complex process but should go relatively quick. Understand that may not be possible though. So that file is the integrated datatypes configuration file I believe. There is just one global copy that gets created with Galaxy boots up - so it cannot be chown-ed on a per job basis. The thing is that Galaxy should be modifying it to be world readable (https://bitbucket.org/galaxy/galaxy-central/annotate/e2b761a9b1d6d41db71b28df8b62862c7c300eba/lib/galaxy/datatypes/registry.py?at=default#cl-811) - something is going wrong if it is not. Can you verify the file is 644? That leads me to believe that users don't have read access to the global temp directory. Can you check if users can read /panfs/storage.local/scratch/galaxy-data/tmp/? I think they will need to to use some tools including uploads? If you cannot make this directory accessible to users - can you change Galaxy's new_file_path so that it is some directory globally readable? -John On Tue, Jun 10, 2014 at 4:10 PM, Shrum, Donald C dcsh...@admin.fsu.edu wrote: Hi all, I'm working with a problem with user uploaded files. After digging through the logs a bit and running the commands on at a time manually I think I've narrowed it to a permissions problem. This was confirmed by just running galaxy as root and the problem went away ;) -bash-4.1$ PYTHONPATH=/panfs/storage.local/software/galaxy-dist/lib/ -bash-4.1$ python /panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py /panfs/storage.local/software/galaxy-dist//panfs/storage.local/scratch/galaxy-data/tmp/tmpSuHquR /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf 6:/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/6/dataset_6_files:/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/6/galaxy_dataset_6.dat Traceback (most recent call last): File /panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py, line 394, in module __main__() File /panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py, line 369, in __main__ registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] ) File /panfs/storage.local/software/galaxy-dist/lib/galaxy/datatypes/registry.py, line 97, in load_datatypes tree = galaxy.util.parse_xml( config ) File /panfs/storage.local/software/galaxy-dist/lib/galaxy/util/__init__.py, line 154, in parse_xml tree = ElementTree.parse(fname) File build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py, line 859, in parse File build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py, line 576, in parse IOError: [Errno 13] Permission denied: '/panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf' -bash-4.1$ ls -l /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf -rw--- 1 dcshrum dcshrum 317 Jun 10 16:30 /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf It does not look like galaxy is using sudo to run the script. Suggestions to work this out? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] upload problems
Hi Jon and thanks for the reply.I am attempting to run jobs as the real user as jobs will go to our HPC cluster. This will be an enterprise server. /panfs/storage.local/scratch/galaxy-data/ is world writable- drwxrwxrwx 4 galaxy galaxy 4096 May 7 09:08 galaxy-data as is tmp -bash-4.1$ ls -l /panfs/storage.local/scratch/galaxy-data/ total 160 drwxrwxrwx 2 galaxy galaxy 20480 Jun 10 17:00 tmp I got a little lost on the integrated datatypes configuration file... is that an XML file? I'm not sure which file I'm looking for and I'm new to galaxy. --Donny -Original Message- From: John Chilton [mailto:jmchil...@gmail.com] Sent: Tuesday, June 10, 2014 5:33 PM To: Shrum, Donald C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] upload problems You didn't include this context, but I am guessing you are attempting to run jobs as the real user? If not, ignore the rest of the e-mail. I would generally not recommend running the uploads as real user - it is a complex process but should go relatively quick. Understand that may not be possible though. So that file is the integrated datatypes configuration file I believe. There is just one global copy that gets created with Galaxy boots up - so it cannot be chown-ed on a per job basis. The thing is that Galaxy should be modifying it to be world readable (https://bitbucket.org/galaxy/galaxy-central/annotate/e2b761a9b1d6d41db71b28df8b62862c7c300eba/lib/galaxy/datatypes/registry.py?at=default#cl-811) - something is going wrong if it is not. Can you verify the file is 644? That leads me to believe that users don't have read access to the global temp directory. Can you check if users can read /panfs/storage.local/scratch/galaxy-data/tmp/? I think they will need to to use some tools including uploads? If you cannot make this directory accessible to users - can you change Galaxy's new_file_path so that it is some directory globally readable? -John On Tue, Jun 10, 2014 at 4:10 PM, Shrum, Donald C dcsh...@admin.fsu.edu wrote: Hi all, I'm working with a problem with user uploaded files. After digging through the logs a bit and running the commands on at a time manually I think I've narrowed it to a permissions problem. This was confirmed by just running galaxy as root and the problem went away ;) -bash-4.1$ PYTHONPATH=/panfs/storage.local/software/galaxy-dist/lib/ -bash-4.1$ python /panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py /panfs/storage.local/software/galaxy-dist//panfs/storage.local/scratch/galaxy-data/tmp/tmpSuHquR /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf 6:/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/6/dataset_6_files:/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/6/galaxy_dataset_6.dat Traceback (most recent call last): File /panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py, line 394, in module __main__() File /panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py, line 369, in __main__ registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] ) File /panfs/storage.local/software/galaxy-dist/lib/galaxy/datatypes/registry.py, line 97, in load_datatypes tree = galaxy.util.parse_xml( config ) File /panfs/storage.local/software/galaxy-dist/lib/galaxy/util/__init__.py, line 154, in parse_xml tree = ElementTree.parse(fname) File build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py, line 859, in parse File build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py, line 576, in parse IOError: [Errno 13] Permission denied: '/panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf' -bash-4.1$ ls -l /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf -rw--- 1 dcshrum dcshrum 317 Jun 10 16:30 /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf It does not look like galaxy is using sudo to run the script. Suggestions to work this out? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Toolshed upload error message
Hi Greg, When I trying to upload a next release version o my https://toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf converter program to Community Toolshed, I am getting an internal error message. I am uploading a tar.gz file to the page https://toolshed.g2.bx.psu.edu/ but this fails. Could you please pass the error message or let me how I can add new files to the repository and delete the old version. Thanks, Vipin | Rätsch Lab ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Non-admin tool install/import
On Tue, Jun 10, 2014 at 7:37 AM, Karthik Gururaj gururaj.kart...@gmail.com wrote: Thanks - will take a look at the Tool Shed and see if there is anything there we can use in safe manner. Else, the old fashioned way of asking users to test out on their tools on a standalone Galaxy system and then requesting the administrator to pull in the relevant XML files. Sorry this is a bit confusing... Just to be quite clear: The Tool Factory is available from the main Tool Shed, but Tool Factory =/= Tool Shed !! The Tool Factory is just another Galaxy tool administrators can use to run scripts interactively in Galaxy. It installs automatically from the main Tool Shed and optionally generates new Galaxy tools from working scripts. New generated tools are in a tgz archive ready to be uploaded into Tool Shed repositories. The Tool Shed is a specialised web server that supports version control and management of Galaxy tool source code and automated installation into Galaxy instances. You could run a local Tool Shed and yes, your admins could use it to install properly configured user provided tools. The Tool Factory allows your scripting-capable users of creating new Galaxy tools from scripts if they run it as administrators of their own laptop/development instances, or your administrators could use it to run scripts directly on your private instance and optionally generate new safe tools (by uploading the archives to your local tool shed then installing those new tools into your local Galaxy) for ordinary users to use in their workflows. Thanks, Karthik On Sun, Jun 8, 2014 at 6:25 PM, Ross ross.laza...@gmail.com wrote: Hi, Karthik and John. Some details on the tool factory for anyone interested. Executive summary: it may be helpful in this context but only for trusted administrators. TL;DR: Firstly, it will refuse to run for anyone other than a local Galaxy administrator. This is because it exposes unrestricted scripting so should only be installed if you can trust your administrative users not to run cd /; rm -rf *. I'd advise installing ONLY on your own private instance and NEVER on a public Galaxy. Secondly, it has two modes of operation - script running and tool generation. When executed without the option to generate a tool archive, it will run a pasted (perl, python, R, bash) script creating an output in the history. This history output is re-doable in the usual Galaxy way including allowing the script to be edited and rerun, so it's possible to (eg) get a script working interactively - galaxy as an IDE anyone ? :) Once a script runs on some test data, the tool factory will optionally generate a complete tool shed compatible gzip which can be uploaded to any tool shed as a new or updated repository. The generated tool includes the supplied test data as a proper Galaxy functional test. Once a tool is in a toolshed, it is just another Galaxy tool, ready to be installed to any Galaxy like any other tool - but will require restarting of multiple web processes as John mentions. If the script is safe, the tool is safe - there are no specific security risks for tool factory generated tools other than the script itself. Finally, currently it takes only one input and generates one output which is a substantial restriction - but of course the generated tool source code is easy to edit if you need more complex I/O. It has a really neat option to create a simple but useful HTML display with links and thumbnails to arbitrary (eg) pdf or other output files from a script - the tool form includes examples in all 4 scripting languages ready to cut and paste, including one which generates 50 random images and presents them in a grid as an HTML page for the user. On Mon, Jun 9, 2014 at 10:32 AM, John Chilton jmchil...@gmail.com wrote: Galaxy doesn't really support this use case and it will be major effort to get it work this way I suspect. Pieces to look at include: The Galaxy Tool Factory (it has the ability to create reusable tools from scripts): http://www.ncbi.nlm.nih.gov/pubmed/23024011 You may be able to modify it in such a way that each tool is tagged with who created and then use ToolBox filters to limit added tools to a given user: https://wiki.galaxyproject.org/UserDefinedToolboxFilters I think the latest version of Galaxy has improved support for adding tools without requiring restarts (using message queues). I don't know if this will automatically work with the tool factory or not. I suspect fighting Galaxy at every step on this will frustrate you and the users - and you are exposing all of your users data to every user you give this privilege to. Is this a shared cluster or is dedicated to Galaxy? If it is shared - it might be better for advanced users to just get importing and exporting data to user directories really well. In my previous position at MSI we created a set of tools that allowed Galaxy to SCP files as the user to
Re: [galaxy-dev] Non-admin tool install/import
Sorry, I meant Tool Factory when I wrote Tool Shed in my previous email. On Tue, Jun 10, 2014 at 5:25 PM, Ross ross.laza...@gmail.com wrote: On Tue, Jun 10, 2014 at 7:37 AM, Karthik Gururaj gururaj.kart...@gmail.com wrote: Thanks - will take a look at the Tool Shed and see if there is anything there we can use in safe manner. Else, the old fashioned way of asking users to test out on their tools on a standalone Galaxy system and then requesting the administrator to pull in the relevant XML files. Sorry this is a bit confusing... Just to be quite clear: The Tool Factory is available from the main Tool Shed, but Tool Factory =/= Tool Shed !! The Tool Factory is just another Galaxy tool administrators can use to run scripts interactively in Galaxy. It installs automatically from the main Tool Shed and optionally generates new Galaxy tools from working scripts. New generated tools are in a tgz archive ready to be uploaded into Tool Shed repositories. The Tool Shed is a specialised web server that supports version control and management of Galaxy tool source code and automated installation into Galaxy instances. You could run a local Tool Shed and yes, your admins could use it to install properly configured user provided tools. The Tool Factory allows your scripting-capable users of creating new Galaxy tools from scripts if they run it as administrators of their own laptop/development instances, or your administrators could use it to run scripts directly on your private instance and optionally generate new safe tools (by uploading the archives to your local tool shed then installing those new tools into your local Galaxy) for ordinary users to use in their workflows. Thanks, Karthik On Sun, Jun 8, 2014 at 6:25 PM, Ross ross.laza...@gmail.com wrote: Hi, Karthik and John. Some details on the tool factory for anyone interested. Executive summary: it may be helpful in this context but only for trusted administrators. TL;DR: Firstly, it will refuse to run for anyone other than a local Galaxy administrator. This is because it exposes unrestricted scripting so should only be installed if you can trust your administrative users not to run cd /; rm -rf *. I'd advise installing ONLY on your own private instance and NEVER on a public Galaxy. Secondly, it has two modes of operation - script running and tool generation. When executed without the option to generate a tool archive, it will run a pasted (perl, python, R, bash) script creating an output in the history. This history output is re-doable in the usual Galaxy way including allowing the script to be edited and rerun, so it's possible to (eg) get a script working interactively - galaxy as an IDE anyone ? :) Once a script runs on some test data, the tool factory will optionally generate a complete tool shed compatible gzip which can be uploaded to any tool shed as a new or updated repository. The generated tool includes the supplied test data as a proper Galaxy functional test. Once a tool is in a toolshed, it is just another Galaxy tool, ready to be installed to any Galaxy like any other tool - but will require restarting of multiple web processes as John mentions. If the script is safe, the tool is safe - there are no specific security risks for tool factory generated tools other than the script itself. Finally, currently it takes only one input and generates one output which is a substantial restriction - but of course the generated tool source code is easy to edit if you need more complex I/O. It has a really neat option to create a simple but useful HTML display with links and thumbnails to arbitrary (eg) pdf or other output files from a script - the tool form includes examples in all 4 scripting languages ready to cut and paste, including one which generates 50 random images and presents them in a grid as an HTML page for the user. On Mon, Jun 9, 2014 at 10:32 AM, John Chilton jmchil...@gmail.com wrote: Galaxy doesn't really support this use case and it will be major effort to get it work this way I suspect. Pieces to look at include: The Galaxy Tool Factory (it has the ability to create reusable tools from scripts): http://www.ncbi.nlm.nih.gov/pubmed/23024011 You may be able to modify it in such a way that each tool is tagged with who created and then use ToolBox filters to limit added tools to a given user: https://wiki.galaxyproject.org/UserDefinedToolboxFilters I think the latest version of Galaxy has improved support for adding tools without requiring restarts (using message queues). I don't know if this will automatically work with the tool factory or not. I suspect fighting Galaxy at every step on this will frustrate you and the users - and you are exposing all of your users data to every user you give this privilege to. Is this a shared cluster or is dedicated to Galaxy? If it is shared - it might be better for advanced users to just
