[galaxy-dev] Uploading Multiple files
Hi, It was suggested recently that Galaxy would soon be providing the ability to upload multiple files rather than single files. Does anyone know when this might be available in Galaxy? I've downloaded the most recent version of Galaxy but as yet it is not present in the "stable" version Thanks for any information Neil ___ 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] Workflow with many inputs
Hi all, I have a tool that receives multiple inputs, and it is working fine if I run it stand alone. However, I want to create a workflow where this tool receive as an input the output of other tools. I can connect the output from the other tools in the input of this tool, but the tool receives only one input. Is there a way to set multiple inputs to a tool in a workflow? I've found several similar questions like mine, but I haven't found an answer. I appreciate your help. Best regards, -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP ___ 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] Toolshed roadmap
Hello Eric, The Tool Shed wiki is currently undergoing significant changes which will hopefully result in an improved set of documentation. This is a high priority between now and October ( see https://trello.com/c/Gg0jnll7/191-wiki-improvements and https://trello.com/c/uHyAaCLT/176-tasks-for-completion-by-october-2014). In the meantime, you may find my blog posts to be helpful ( see http://gregvonkuster.org ) Greg Von Kuster On Jul 15, 2014, at 4:00 PM, Eric Rasche wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Hi Greg, > > Sorry about that, toolshed development hasn't been very visible in my > view of galaxy thus far, so it seemed like asking someone who knew would > be the fastest route here. I'll ensure my future inquires go to galaxy-dev. > > On 07/15/2014 02:18 PM, Greg Von Kuster wrote: >> Hello Eric, >> >> Please use Biostar or the Galaxy dev mail list rather than individual email >> addresses in order to ensure faster responses. Pleasse see my responses >> below. >> >> On Jul 14, 2014, at 10:20 AM, Eric Rasche wrote: >> >> Howdy Greg, >> >> Since there isn't really a public/published roadmap and you're the >> toolshed guy, I'm emailing to see if I can find out what's in the >> toolshed's future. >> >>> The tool shed Trello board at >>> https://trello.com/b/vHqpKpZF/galaxy-tool-shed is the roadmap for the Tool >>> Shed. Just like the Galaxy Development Trello board, you should be able to >>> add new cards to the Inbox, and vote on existing cards to raise their >>> priority. Please let us know if you are not able to do these things. > > I was not aware that a trello board even existed for the toolshed, that > would have answered some of these. > > (It might be good to have it mentioned more than once on the wiki, > perhaps under "Toolshed" and not just under "Issues") > >> Specifically, I'm wondering if there will be API calls for the following >> things: >> >> - creating repositories >> >>> I've added the following Trello card for the above feature. However, it is >>> currently possible to create new repositories via the API by importing a >>> repository capsule (i.e., ~/api/repositories/import_capsule). >> >>> https://trello.com/c/cUUWeBCi/234-enhance-the-api-to-enable-creation-of-new-repositories >> >> - obtaining a list of categories >> >>> The above was introduced in the June 2, 2014 release, so, for example, the >>> following will work. >> >>> https://testtoolshed.g2.bx.psu.edu/api/categories > > Are any of these API changes documented outside of > mercurial/DevNewsBriefs (trello)? > > My go-to locations for documentation are the wiki and readthedocs. > > Neither https://wiki.galaxyproject.org/ToolShedApi > or > http://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.tool_shed.api.html > > has up-to-date documentation. Is there another place I should be looking > for static, complete toolshed API information? > >> - obtaining category information within the /api/repositories call >> >>> I've added the following Trello card for this feature. >> >>> https://trello.com/c/n7P0GE1P/235-enhance-the-api-repositories-feature > > Thanks! > >> >> >> >> Cheers, >> Eric >> >> > > Cheers, > Eric > -BEGIN PGP SIGNATURE- > Version: GnuPG v2.0.22 (GNU/Linux) > > iQIcBAEBAgAGBQJTxYhAAAoJEMqDXdrsMcpV9K0QAKd/KIFxXLmfx1gj208GwCCl > WCugrb7F1jKvGMTz+IkyqaFlSsC+d5PjFskETEPIlUjIsXFQ1EwHKQWDVTDRjwEV > r9H0huCwfhvS0xz4wlHcrkHBimWCktlfqnbbCzmAkmNuqQ3e2zPquvVajQlcUFQM > rVjbn45+c6C2ewy8JeOB9bJUG4JbtIH3jeFWreu8UiBFn8WcfkAsEigDoluLzgpg > JuakNPrMuzrVqlsvfJw+Pv0xbYntplrfTOAV1G5F1Qbyc0Zb9KoH5cHKTfIf8bNS > E4g2Djvr/ow+ofsf88floBjTfsLUy6ck1/LaAgbwyDIY8b4IVrv3SgtyL6mLx+FX > 8K/WvbPgQH7adDykUkMLRwfQcrkTdws1uGYf6EQwqGr0P1KqDcCQufH8y9MH24If > Sn51+UlceOR2uQEIi7x8Xm6/tPsIcN+MUrWb//FzrLDitHaGLCZRLGRxrQyACkXS > 9IfM9tz6aqR6b8OrEcUGo4E+6azpHsQgi2iTnQz2tVT4g1viKYmwKoPTT58Cm6KF > 7h32taJMGabZm618bB/DOT8jxxfZ2VfEfXgMFZaSpkIbMsXnnaS5Pivtwxl7R1nP > Sw73Pm2sBNsrnpPjQph39jS2rj1Oqb9PbH8k4EJl36fNiZAksNsi7n5cOCka1P66 > 2lyxcFTRAwic0CwTJ5Vx > =S+xu > -END PGP SIGNATURE- ___ 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] Toolshed roadmap
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Greg, Sorry about that, toolshed development hasn't been very visible in my view of galaxy thus far, so it seemed like asking someone who knew would be the fastest route here. I'll ensure my future inquires go to galaxy-dev. On 07/15/2014 02:18 PM, Greg Von Kuster wrote: > Hello Eric, > > Please use Biostar or the Galaxy dev mail list rather than individual email > addresses in order to ensure faster responses. Pleasse see my responses > below. > > On Jul 14, 2014, at 10:20 AM, Eric Rasche wrote: > > Howdy Greg, > > Since there isn't really a public/published roadmap and you're the > toolshed guy, I'm emailing to see if I can find out what's in the > toolshed's future. > >> The tool shed Trello board at https://trello.com/b/vHqpKpZF/galaxy-tool-shed >> is the roadmap for the Tool Shed. Just like the Galaxy Development Trello >> board, you should be able to add new cards to the Inbox, and vote on >> existing cards to raise their priority. Please let us know if you are not >> able to do these things. I was not aware that a trello board even existed for the toolshed, that would have answered some of these. (It might be good to have it mentioned more than once on the wiki, perhaps under "Toolshed" and not just under "Issues") > Specifically, I'm wondering if there will be API calls for the following > things: > > - creating repositories > >> I've added the following Trello card for the above feature. However, it is >> currently possible to create new repositories via the API by importing a >> repository capsule (i.e., ~/api/repositories/import_capsule). > >> https://trello.com/c/cUUWeBCi/234-enhance-the-api-to-enable-creation-of-new-repositories > > - obtaining a list of categories > >> The above was introduced in the June 2, 2014 release, so, for example, the >> following will work. > >> https://testtoolshed.g2.bx.psu.edu/api/categories Are any of these API changes documented outside of mercurial/DevNewsBriefs (trello)? My go-to locations for documentation are the wiki and readthedocs. Neither https://wiki.galaxyproject.org/ToolShedApi or http://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.tool_shed.api.html has up-to-date documentation. Is there another place I should be looking for static, complete toolshed API information? > - obtaining category information within the /api/repositories call > >> I've added the following Trello card for this feature. > >> https://trello.com/c/n7P0GE1P/235-enhance-the-api-repositories-feature Thanks! > > > > Cheers, > Eric > > Cheers, Eric -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (GNU/Linux) iQIcBAEBAgAGBQJTxYhAAAoJEMqDXdrsMcpV9K0QAKd/KIFxXLmfx1gj208GwCCl WCugrb7F1jKvGMTz+IkyqaFlSsC+d5PjFskETEPIlUjIsXFQ1EwHKQWDVTDRjwEV r9H0huCwfhvS0xz4wlHcrkHBimWCktlfqnbbCzmAkmNuqQ3e2zPquvVajQlcUFQM rVjbn45+c6C2ewy8JeOB9bJUG4JbtIH3jeFWreu8UiBFn8WcfkAsEigDoluLzgpg JuakNPrMuzrVqlsvfJw+Pv0xbYntplrfTOAV1G5F1Qbyc0Zb9KoH5cHKTfIf8bNS E4g2Djvr/ow+ofsf88floBjTfsLUy6ck1/LaAgbwyDIY8b4IVrv3SgtyL6mLx+FX 8K/WvbPgQH7adDykUkMLRwfQcrkTdws1uGYf6EQwqGr0P1KqDcCQufH8y9MH24If Sn51+UlceOR2uQEIi7x8Xm6/tPsIcN+MUrWb//FzrLDitHaGLCZRLGRxrQyACkXS 9IfM9tz6aqR6b8OrEcUGo4E+6azpHsQgi2iTnQz2tVT4g1viKYmwKoPTT58Cm6KF 7h32taJMGabZm618bB/DOT8jxxfZ2VfEfXgMFZaSpkIbMsXnnaS5Pivtwxl7R1nP Sw73Pm2sBNsrnpPjQph39jS2rj1Oqb9PbH8k4EJl36fNiZAksNsi7n5cOCka1P66 2lyxcFTRAwic0CwTJ5Vx =S+xu -END PGP SIGNATURE- ___ 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] Toolshed roadmap
Hello Eric, Please use Biostar or the Galaxy dev mail list rather than individual email addresses in order to ensure faster responses. Pleasse see my responses below. On Jul 14, 2014, at 10:20 AM, Eric Rasche wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Howdy Greg, > > Since there isn't really a public/published roadmap and you're the > toolshed guy, I'm emailing to see if I can find out what's in the > toolshed's future. The tool shed Trello board at https://trello.com/b/vHqpKpZF/galaxy-tool-shed is the roadmap for the Tool Shed. Just like the Galaxy Development Trello board, you should be able to add new cards to the Inbox, and vote on existing cards to raise their priority. Please let us know if you are not able to do these things. > > Specifically, I'm wondering if there will be API calls for the following > things: > > - - creating repositories I've added the following Trello card for the above feature. However, it is currently possible to create new repositories via the API by importing a repository capsule (i.e., ~/api/repositories/import_capsule). https://trello.com/c/cUUWeBCi/234-enhance-the-api-to-enable-creation-of-new-repositories > - - obtaining a list of categories The above was introduced in the June 2, 2014 release, so, for example, the following will work. https://testtoolshed.g2.bx.psu.edu/api/categories > - - obtaining category information within the /api/repositories call I've added the following Trello card for this feature. https://trello.com/c/n7P0GE1P/235-enhance-the-api-repositories-feature > > Cheers, > Eric > > - -- > Eric Rasche > Programmer II > Center for Phage Technology > Texas A&M University > College Station, TX 77843 > 404-692-2048 > e...@tamu.edu > rasche.e...@yandex.ru > -BEGIN PGP SIGNATURE- > Version: GnuPG v2.0.22 (GNU/Linux) > > iQIcBAEBAgAGBQJTw+dEAAoJEMqDXdrsMcpVKJ0P/0cJVIeFZ4NXmR0IPgMsQBMK > j6yw4rk69iUBgS0phk19kHaOi4kQtsrlwtpled13MEWBL2MBcHSFSHGn8RsvH1pW > JzbbQiFN/AOycTaDnV91veG3JuJ2MHAA2IAzx+fyjqlZV5ekZfK1q3xYB0E7EKyl > iojoqP5ewa8FC29LB0TnAswmEA384S6sPmqUicRmL5m0QR6hBBCf44nfN/Zvl2iw > ZqdKovO1EZBJ4vEHhZnN4rAdvFnqhghBOB/mjoKVGMIsJvu3I66PxhV+VhFdoLKJ > yaSWWAd3gwp0gP8NDEunDRkF1rM0eJgVou9eUtPPQkxun5S7c7bACMYdhmpyCcVu > wgNE2UnP0x1EFDx8q77WmT78nMp7khxWU8Q/3YPoGTr4r3DfSYrvMqD81uoIvkBJ > MqB89mJS2VqHi88idzIlyIYP3CE7mDEjDcHpLonY+uFxc3LNQEOcP0pvvPpNTkmw > Oix60X+GSACH0s8lqlInzEhu1OqbW0nokAayvDmzYjmttrVOFqQdhUFTYxq7El5M > yXE31fX+VTHnIbx/ZPSvl1TqbldrTFs/J4KnvNbf4PuseLQDRmsnrFJ7lSii2xSc > imqQiwyt7lCRHCO5+w+jSaMUPQ3SrbGxsbAckqK+HkCllJ87v7oC1CBLugOP5425 > 2E7ad35BvZ1bGmumAw9q > =ZXxZ > -END PGP SIGNATURE- ___ 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] Toolshed : tool_dependency xml, action problem
Are the problems described in this thread occurring with the latest Galaxy
release? The references to the code lines do not seem to reflect the latest
Galaxy release.
Thanks,
Greg Von Kuster
On Jul 7, 2014, at 10:34 AM, Nicolas Lapalu
wrote:
> Hi
>
> There's a bug in the
> "galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py" file.
> line 79 : dir can be equal to None, but os.path.join() raises an error with
> an arg equal to None
> To fix it :
> if dir == None:
>dir = ''
>
> nico
>
> Le 07/07/2014 14:38, Kandalaft, Iyad a écrit :
>> That error sounds like it's trying to merge the current working directory
>> with the path supplied in the "CHMOD" tag.
>> current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) <-- join
>> work_dir with dir
>>
>> You have 2 possibilities to try:
>> 1. Eliminate the $INSTALLDIR from the path in the XML if you're already in
>> that path
>> 2. Changedir to the path before trying the CHMOD tag and use "." as the path
>>
>>
>> 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
>>
>>
>>
>> -Original Message-
>> From: galaxy-dev-boun...@lists.bx.psu.edu
>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nicolas Lapalu
>> Sent: Monday, July 07, 2014 5:57 AM
>> To: galaxy-dev@lists.bx.psu.edu
>> Subject: [galaxy-dev] Toolshed : tool_dependency xml, action problem
>>
>> Hi all,
>>
>> I'm trying to package my tool wrapper to release it in the ToolShed. I need
>> to download the associated binary file and change the permissions.
>> I wrote a tool_dependency xml file with a downlod_binary and chmod actions.
>> My tool_dependency_dir is well defined in my universe file. The download is
>> ok, but I get an error during the "chmod" action.
>> So I tried with your example, faToTwoBit
>> (https://wiki.galaxyproject.org/DownloadingBinaries), and I get the same
>> bug. Do you know the problem ? Do I need to configure someting else ?
>>
>> log :
>>
>> tool_shed.util.tool_dependency_util DEBUG 2014-07-07 11:28:34,346 Updating
>> an existing record for version 0.0.1 of tool dependency faToTwoBit for
>> revision 5ac8ed26842c of repository mytool by updating the status from Never
>> installed to Installing.
>> tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG
>> 2014-07-07 11:28:34,374 Attempting to download from
>> http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit to bin
>> 127.0.0.1 - - [07/Jul/2014:11:28:36 +0200] "POST
>> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 -
>> "http://127.0.0.1:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0
>> (X11; Linux x86_64; rv:24.0) Gecko/20140610 Firefox/24.0 Iceweasel/24.6.0"
>> tool_shed.galaxy_install.install_manager ERROR 2014-07-07 11:28:39,038 Error
>> installing tool dependency faToTwoBit version 0.0.1.
>> Traceback (most recent call last):
>>File
>> "/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
>> line 110, in install_and_build_package_via_fabric
>> tool_dependency = self.install_and_build_package( app,
>> tool_shed_repository, tool_dependency, actions_dict )
>>File
>> "/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
>> line 79, in install_and_build_package
>> current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
>>File "/usr/lib/python2.7/posixpath.py", line 75, in join
>> if b.startswith('/'):
>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>
>> Thanks for your help;
>> nico
>> ___
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>> 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/
>
> ___
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> http://lists.bx.psu.edu/
>
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>
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Re: [galaxy-dev] writing datatypes
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Peter, I saw that in an initial search for genbank modules, however it didn't meet our requirements (lack of features/"heavy" by requiring all of emboss). And, you are correct, it doesn't fix the problem. Thanks for the suggestion. Cheers, Eric On 07/15/2014 03:14 AM, Peter Cock wrote: > Hi Eric > > There is already a genbank format in the EMBOSS datatypes > (although there is talk of defining this and others in a set of > smaller repositories defined as its dependencies for more > modularity). Note it uses "genbank" not "gb" as the name! > > https://toolshed.g2.bx.psu.edu/view/devteam/emboss_datatypes > > However that doesn't answer your question :( > > Peter > > On Mon, Jul 14, 2014 at 7:31 PM, Eric Rasche wrote: > I'm trying to add a new datatype to my galaxy instance for genbank > files, however I'm running into various issues. I've followed the > tutorial (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes) > > however that example subclasses tabular, and I'd like to subclass Text > as they're plain text files, and I'd like to be able to define a sniffer > for them (not possible if your type=galaxy.datatypes.data:Text) > > I figured the call ought to be something like > > subclass="True" /> > > however, everything I try fails with > Error importing datatype module galaxy.datatypes.data: 'module' object has no attribute 'Genbank' > > To avoid this particular issue, I tried writing a separate datatype just > for genbank files (type="galaxy.datatypes.genbank:Genbank"), however > that fails with the same error: > galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error importing datatype module galaxy.datatypes.genbank: 'module' object has no attribute 'genbank' Traceback (most recent call last): File "/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py", line 206, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'genbank' > > Here's my lib/galaxy/datatypes/genbank.py looks like: > import pkg_resources pkg_resources.require( "bx-python" ) import logging from galaxy.datatypes import data log = logging.getLogger(__name__) class Genbank( data.Text ): file_ext = "gb" def sniff( self, filename ): header = open(filename).read(5) return header == 'LOCUS' > > To debug this, I've tried copying the tabular data type completely, > removed all the classes other than Tabular, and renamed it "Genbank", > however this fails too with the same error. > > Can anyone offer some insight? > > Cheers, > Eric >> ___ >> 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/ -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (GNU/Linux) iQIcBAEBAgAGBQJTxULLAAoJEMqDXdrsMcpVtsAP/j8i8rNcrJqgOCnYexD2dHoQ yn6JYRQRNziJrqhwVTuH1i47rFJXUoo2whaD4QKwSnrXg0iQSpSgiM74e+IKmOFQ lnqyQQP50YHMars3U9441T15GcSSpNEW1FwxtBIrIt76bV26BPx+YKqhukA76eQ8 e5X+HRPsFu8+jczL0zcAv5DGSmskoJz6wDc9jlaWbFu21mjPPZiY6FFdXZaBR/h2 AesD68P85d4sygzcE42BDuSUg2obPSiBA5DJ/CMWlUNDeZi4V6/KO/F2LmC2PAak rR9xSSS2HXryuqREzRX8Ny1jq6Y0v34zTjObwtWTExE2olTPqPxB0pvEsaoKFis7 KNEP9qLgOMTKjCTzrb1qRgQ5Iq5utNP0TyYEWGQKolpGA1L7updETFfQBw9PY2pu /w8EkRzd6zermy2cQFYRKgvR081R6jwngJV4UUG2FXH6+bFAK4knpQ1+fT0/2PoD qIxnB5bEUW00RiJRnKbMCWoepcl4CAQepLdgHa0ofYMNkPsZIi2mR6DBv49HRx9v P56TRNfXDYW0nyoFRkQKNlMafjWg8ykOUsHVAcC++uicCLebWWHrQWNMEsWQr7Qk QIg1YLhejYK1Lfiafqnu23xMat2TVS149w4bik9VNhvtIxImOvoXCpU5EpDCq2BG gCTFHSzb7/kS3yvj1EQQ =qop5 -END PGP SIGNATURE- ___ 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] How to configure galaxy with a cluster
Hello Ben, you can configure your Galaxy instance to use your cluster in the job_conf.xml file: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster You can set up your instance to use your cluster by default for all jobs or only for specific jobs. Here is a part of my job_conf.xml for example: -r yes -b n -cwd -S /bin/bash -V -pe galaxy 1 -r yes -b n -cwd -S /bin/bash -V -pe galaxy 12 Moreover you Galaxy user and Galaxy server must be allowed to submit jobs to your scheduler. Hope it helps, Thomas -- Thomas Bellembois, Network and System Administrator ENS-Lyon/IGFL - FRANCE +33 4 26 73 13 67 .The IGFL is a member of the "portail-labos" project (https://portail-labos.ens-lyon.fr/site/). .IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc On 15/07/2014 11:22, 王渭巍 wrote: > Hello, everyone, > I am new here, and I am trying to configure galaxy with a cluster. > I have 3 servers. One for galaxy server, two for cluster computing. > And I followed "Running Galaxy Tools on a Cluster" done the configuration. > Now I have 2 questions: > 1. How to vertify whether I have configured the galaxy cluster > successfully? For example, I don't see there is any cluster options in "NGS > mapping (bowtie2) ", but I see cluster options in a web galaxy. > 2. And any other work I should do for configuring galaxy with a > cluster? > Thank you for any help. > > Ben > > > > ___ > 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] How to configure galaxy with a cluster
Hello, everyone, I am new here, and I am trying to configure galaxy with a cluster. I have 3 servers. One for galaxy server, two for cluster computing. And I followed "Running Galaxy Tools on a Cluster" done the configuration. Now I have 2 questions: 1. How to vertify whether I have configured the galaxy cluster successfully? For example, I don't see there is any cluster options in "NGS mapping (bowtie2) ", but I see cluster options in a web galaxy. 2. And any other work I should do for configuring galaxy with a cluster? Thank you for any help. Ben ___ 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] API v/s twill based testing
Hi Saket, >From memory the Twill tests are fragile with the output file order in the XML. John was discussing switching the default from the Twill to API backend, not sure when that is happening though... Peter On Tue, Jul 15, 2014 at 9:31 AM, Saket Choudhary wrote: > I recently updated tests for one of my wrappers and came across this strange > behaviour: > > The twill based testing reports a failure: > https://travis-ci.org/saketkc/galaxy_tools/jobs/29956682#L1463 > > whereas, the API based testing shows success: > https://travis-ci.org/saketkc/galaxy_tools/jobs/29956683 > > Unfortunately I cannot run these tests locally since I am behind a system > proxy [Refer: > http://dev.list.galaxyproject.org/Functional-Tests-and-ftype-td4664233.html] > and have to rely on travis.. > > The place where twii tests fails shows that it is trying to compare the > diff between 'chasm_output_genes.tabular' and > 'chasm_output_variants.tabular' instead of 'chasm_output_genes.tabular'. > [See : https://travis-ci.org/saketkc/galaxy_tools/jobs/29956682#L1469] > > I tried running my tools locally and I did not come across any case where > the 'variants' output gets replaced by the 'genes' output, thus possibly > ruling out unexpected behavior from the tool's server end. > > Is this a possible bug or am I missing something? > > Saket > > ___ > 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] API v/s twill based testing
I recently updated tests for one of my wrappers and came across this strange behaviour: The twill based testing reports a failure: https://travis-ci.org/saketkc/galaxy_tools/jobs/29956682#L1463 whereas, the API based testing shows success: https://travis-ci.org/saketkc/galaxy_tools/jobs/29956683 Unfortunately I cannot run these tests locally since I am behind a system proxy [Refer: http://dev.list.galaxyproject.org/Functional-Tests-and-ftype-td4664233.html] and have to rely on travis.. The place where twii tests fails shows that it is trying to compare the diff between 'chasm_output_genes.tabular' and 'chasm_output_variants.tabular' instead of 'chasm_output_genes.tabular'. [See : https://travis-ci.org/saketkc/galaxy_tools/jobs/29956682#L1469] I tried running my tools locally and I did not come across any case where the 'variants' output gets replaced by the 'genes' output, thus possibly ruling out unexpected behavior from the tool's server end. Is this a possible bug or am I missing something? Saket ___ 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] writing datatypes
Hi Eric There is already a genbank format in the EMBOSS datatypes (although there is talk of defining this and others in a set of smaller repositories defined as its dependencies for more modularity). Note it uses "genbank" not "gb" as the name! https://toolshed.g2.bx.psu.edu/view/devteam/emboss_datatypes However that doesn't answer your question :( Peter On Mon, Jul 14, 2014 at 7:31 PM, Eric Rasche wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > I'm trying to add a new datatype to my galaxy instance for genbank > files, however I'm running into various issues. I've followed the > tutorial (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes) > > however that example subclasses tabular, and I'd like to subclass Text > as they're plain text files, and I'd like to be able to define a sniffer > for them (not possible if your type=galaxy.datatypes.data:Text) > > I figured the call ought to be something like > > subclass="True" /> > > however, everything I try fails with > >> Error importing datatype module galaxy.datatypes.data: 'module' object has >> no attribute 'Genbank' > > To avoid this particular issue, I tried writing a separate datatype just > for genbank files (type="galaxy.datatypes.genbank:Genbank"), however > that fails with the same error: > >> galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error importing >> datatype module galaxy.datatypes.genbank: 'module' object has no attribute >> 'genbank' >> Traceback (most recent call last): >> File "/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py", >> line 206, in load_datatypes >> module = getattr( module, mod ) >> AttributeError: 'module' object has no attribute 'genbank' > > Here's my lib/galaxy/datatypes/genbank.py looks like: > >> import pkg_resources >> pkg_resources.require( "bx-python" ) >> import logging >> from galaxy.datatypes import data >> log = logging.getLogger(__name__) >> >> class Genbank( data.Text ): >> file_ext = "gb" >> >> def sniff( self, filename ): >> header = open(filename).read(5) >> return header == 'LOCUS' > > To debug this, I've tried copying the tabular data type completely, > removed all the classes other than Tabular, and renamed it "Genbank", > however this fails too with the same error. > > Can anyone offer some insight? > > Cheers, > Eric > -BEGIN PGP SIGNATURE- > Version: GnuPG v2.0.22 (GNU/Linux) > > iQIcBAEBAgAGBQJTxCHwAAoJEMqDXdrsMcpVmbsQAJ3eFIhZtZmVP9LCz/F9Ywg/ > 148NJZy4lmxZU0KScJlc8kVDCDSADXIHd0Db/kpJwuUKEX7zei9q2uXfO7sWl3yt > yxrFEdtX/a5SMVsa6F5WZuKwBs0zfvfsnIUoraOgh6nXeJnr53l9mYeWaKB6bi3Z > xAlgJG/kdIR1jRjAimuQf4vMjNgtDQPOmotYBQTytbhsV6/nRzGI8RZAYwQ7GnVs > XYOWFyhzrBgALndVI3BjI21rbRqguhrqr2t7i0Ma7Pp2JmAnNjmUaq70NN3Rueh6 > DvnTtxInM1dVOQY+Yam6MCMmAedV1cG+rNGdpP2l82MajQAsMtbXckBXXKcSgyTq > WCFoLVURYO1tHkWyq4ikamfFDHtJp1DogBYhUiPMyRw+CV+3sOvr0U5DcyRdiDsJ > Xcm3ygqYVLGwauNmuN3yGcQcnfypDOOeFs1lppbNe3lw0w3ikZN4Zmu1ec5s1ITK > MEcgBrGYgZrKDRXkx53lnABGpv6mYflYpag7fguDNL8j0lh9beaaNmHr4tmeEcug > VZ1b1EWoLMj/ikJ/vZcluiHPTSTheiAP8Ttvh1WAayq4rKwVtZygaI9IDauqqBQ1 > Dgotes3vcomlTQXDUEZACyOZDxl7wbAUh0LZVaa2fYNIOoPNPOItUFSjf6YveF88 > dLiw3ddVm+BFmczJzRpt > =4m2j > -END PGP SIGNATURE- > ___ > 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/
