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Re: [galaxy-dev] Best way to work with one directory and many files as 1 input
by Pierre Pericard 01 Feb '13

01 Feb '13

Hi Christos, Yes, I would be very interested by your modified file. I'm forwarding to the mailing-list so this bug can be listed. Thanks, Pierre Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB) Station Biologique de Roscoff CNRS - UPMC Place Georges Teissier CS 90074 29688 ROSCOFF CEDEX FRANCE Tel : (+33) 2 98 29 56 46 http://abims.sb-roscoff.fr/ Le 01/02/2013 00:34, chriskannas(a)gmail.com a écrit : > Hi, > > I'm working on the same thing, having a composite dataset with many files in many sub-folders. > > Well during the development & testing of the tool that uses this composite datatype, I found out that Galaxy does not handle correctly sub-dirs, it works pretty good with files but if it finds a sub-dir then the copy messes it up. > > To be more specific it uses shutil.copy without checking if it is file or directory, when coping dirs it has to use shutil.copytree. > > I managed to make our local Galaxy installation to handle them quite ok with some modifications in method DiskObjectStor.update_from_file(...) located in lib/galaxy/objectstore/__init__.py > > I can send you a copy of the file I've modified. > > Regards, > Christos > > ------ > > Christos Kannas > Researcher > Ph.D Student > > e-Health Laboratory > Dept. Computer Science, > University of Cyprus > > <quote author='Pierre Pericard'> > Ok, thanks a lot, I'll try and get back to the mailing list if other > problems seem to occur. > > Pierre. > > > Pierre Pericard > IE CDD - Projet Peptisan > > Service Informatique et Bio-informatique (SIB) > Station Biologique de Roscoff > CNRS-UPMC > Place Georges Teissier > CS 90074 > 29688 Roscoff CEDEX > FRANCE > http://abims.sb-roscoff.fr/ > > Le 30/01/2013 11:45, Ross a écrit : >> I'd suggest: >> 1) Make your new datatype a subclass of Html - it's a subclass of >> composite that contains an HTML document as the object's native >> display - so it can inform users what's there. >> >> 2) When constructing these new things, pass the file_path of the Html >> (composite) dataset subclass to your wrapper on the command line >> >> 3) Your wrapper code can construct any arbitrary structure as long as >> it's rooted in that directory - Galaxy stores it without any fuss. The >> wrapper should also populate the Html file itself with nicely >> laid annotation for the user to check out. >> >> 4) The key is that all tools that take this new datatype as input must >> know how to decode this structure - they must be passed the >> $input.extra_files_path which gives them that same path root. >> >> 5) Yes, it's odd and annoying that it's extra_files_path for >> files_path. Go figure. >> >> 6) grep extra_files tools/*.xml to find some examples - I think the >> velvetg one uses a complex subdirectory structure - but it doesn't >> really matter - as long as your tools know how to deal with it, it's >> just a directory to Galaxy! >> I hope all this helps... >> >> >> On Wed, Jan 30, 2013 at 8:22 PM, Pierre Pericard >> <pierre.pericard(a)sb-roscoff.fr <mailto:pierre.pericard@sb-roscoff.fr>> >> wrote: >> >> In that case, could anyone point me to an example of a Composite >> Datatype which could accept as input an unknown number of files in >> an unknown number of directories. I can't seem to understand how >> that would work based on the wiki. >> >> But maybe are we anticipating a near functionality of Galaxy. >> There were talks about changing the way Galaxy handle zip files, >> is it still on the table ? >> >> Thank in advance for any help, >> >> Pierre >> >> >> >> Pierre Pericard >> IE CDD - Projet Peptisan >> >> Service Informatique et Bio-informatique (SIB) >> Station Biologique de Roscoff >> CNRS-UPMC >> Place Georges Teissier >> CS 90074 >> 29688 Roscoff CEDEX >> FRANCE >> http://abims.sb-roscoff.fr/ >> >> Le 29/01/2013 18:04, Peter Cock a écrit : >> >> On Tue, Jan 29, 2013 at 4:58 PM, Pierre Pericard >> <pierre.pericard(a)sb-roscoff.fr >> <mailto:pierre.pericard@sb-roscoff.fr>> wrote: >> >> If I'm not mistaking, Composite Datatypes allow for only >> one directory, >> whereas we need to keep a constant directory structure >> with 2 or more >> sub-directories containing our input files. >> >> I'm not sure if that is true - the example of HTML output with >> images >> comes to mind as a common use-case where subfolder(s) would be >> expected. I've only had limited first hand experience with >> Galaxy's >> composite datatypes myself though. >> >> We have no way to change these tools behavior (obviously >> not Galaxy-friendly >> ;-) ) and therefore need to maintain this structure in the >> job working >> directory. >> >> Perhaps a tool wrapper could create a dummy folder using symlinks >> (faster and less wasted disk than copying files), but that >> isn't ideal. >> >> Peter >> >> >> ___________________________________________________________ >> > > ___________________________________________________________ > 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/ > </quote> > Quoted from: > http://dev.list.galaxyproject.org/Best-way-to-work-with-one-directory-and-m…

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uploading big file on local Galaxy
by stefano cardinale 01 Feb '13

01 Feb '13

Hi, I have installed Galaxy on our local server, which is up and running. I have a very big file (>5Gb) which I want to upload and I don't want to use the upload option but rather sftp or use FileZilla, where should I transfer the file to show up in my History? thanks! stefano Cardinale Stefano Postdoctoral researcher Arkin Lab Department of Bioengineering Energy Biosciences Building 2151 Berkeley Way 94720 - Berkeley

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iterating over files
by mark.rose＠syngenta.com 01 Feb '13

01 Feb '13

Hello I've seen posts from a couple of years ago asking about galaxy's ability to iterate over multiple files. The reply was that the developers were working on it. Have they succeeded and if so how can it now be done. Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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how to sftp a file on a local instance of Galaxy
by stefano cardinale 01 Feb '13

01 Feb '13

Hi, I have installed Galaxy on our local server, which is up and running. I have a very big file (>5Gb) which I want to upload and I don't want to use the upload option but rather sftp or use FileZilla, where should I transfer the file to show up in my History? thanks! stefano Cardinale Stefano Postdoctoral researcher Arkin Lab Department of Bioengineering Energy Biosciences Building 2151 Berkeley Way 94720 - Berkeley

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Re: [galaxy-dev] Best way to work with one directory and many files as 1 input (Pierre Pericard)
by Christos Kannas 01 Feb '13

01 Feb '13

Hi, I'm working on the same thing, having a composite dataset with many files in many sub-folders. Well during the development & testing of the tool that uses this composite datatype, I found out that Galaxy does not handle correctly sub-dirs, it works pretty good with files but if it finds a sub-dir then the copy messes it up. To be more specific it uses shutil.copy without checking if it is file or directory, when coping dirs it has to use shutil.copytree. I managed to make our local Galaxy installation to handle them quite ok with some modifications in method DiskObjectStor.update_from_file(...) located in lib/galaxy/objectstore/__init__.py I can send you a copy of the file I've modified. Regards, Christos -- Christos Kannas Researcher Ph.D Student e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/> kannas.christos(a)ucy.ac.cy kannas.christos(a)cs.ucy.ac.cy chriskannas(a)gmail.com

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FW: install reference genome Bwa and Bowtie!
by Hakeem Almabrazi 01 Feb '13

01 Feb '13

-----Original Message----- From: Hakeem Almabrazi Sent: Thursday, January 31, 2013 7:54 AM To: 'Carlos Borroto' Subject: RE: [galaxy-dev] install reference genome Bwa and Bowtie! Thank you Carlos for your help, I was sure that was not the case (all in tabs). Here is my bwa_indices.loc file look like ##################### #bwaReference /usr/local/galaxy_data/hg19/bwa/ hg19_reference_genome /usr/local/galaxy_data/hg19/bwa/hg19_reference_genome.fasta ####################### The same issue is happening with bowtie. Is there anything I need to do somewhere else in the system (DB, configuration files etc) i.e in ~ tool-data/shared/ucsc/builds.txt file. Regards, Hakeem -----Original Message----- From: Carlos Borroto [mailto:carlos.borroto@gmail.com] Sent: Wednesday, January 30, 2013 10:22 PM To: Hakeem Almabrazi Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie! On Wed, Jan 30, 2013 at 7:19 PM, Hakeem Almabrazi <halmabrazi(a)idtdna.com> wrote: > 4. I created the loc files (bowtie_indices.loc and > bowtie_indices_color.loc and bwa_index.loc) and populate them with the > recommended contents) and place them in ~/tool_data/ folder. Most of the time I run into this issue this is the step where I'm messing up. Double check you are using TABs (not spaces) to separate values in these files. Also check you have only one TAB between values, some of the examples have more than one for pretty formatting but that will cause the configuration not to work. Hope it helps, Carlos

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Re: [galaxy-dev] python version
by Dannon Baker 31 Jan '13

31 Jan '13

Hi Kathryn, Hopefully instructions here should help you out: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use… I've also cc'd the galaxy-dev list as that's the best place to ask questions like this instead of emailing team members directly. Using the list, you'll reach a larger audience who may be able to help you and at the same time the answer to your question can benefit others. Let me know if you have any more trouble, -Dannon Sun, Wenping [USA] wrote: Hi Dannon, The python at my server version is 2.4. I have installed python 2.7 and set link as well as path based on the guide. However, the default python version still remain unchanged and galaxy would not run. Would you mind providing some help on this? Thank you very much, Kathryn

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Running a local tool shed - teething trouble
by Peter Cock 31 Jan '13

31 Jan '13

Hi all, I was hoping to make some enhancements to the ToolShed, so first I need to be able to run my own ToolShed locally: http://wiki.galaxyproject.org/HostingALocalToolShed I have the latest code for bitbucket for galaxy-central: $ hg heads default changeset: 9117:04e221996871 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Jan 30 16:47:20 2013 -0500 summary: Dont' assume a complex repository dependency was properly defined. The following cryptic error is not helpful: $ sh run_community.sh Command 'serve' not known (you may need to run setup.py egg_info) No commands registered. Have you installed Paste Script? (try running python setup.py develop) I then noticed that there was no community_wsgi.ini file, and tried using a copy of the sample: $ cp community_wsgi.ini.sample community_wsgi.ini $ sh run_community.sh (runs with no output, finished in 3s) Does it make sense to generate community_wsgi.ini automatically? Or give an explicit error if it is missing? Looking at the log file, I have a Python depenancy issue here: $ more community_webapp.log ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/builds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ensembl/builds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ncbi/builds.txt' WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Traceback (most recent call last): File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/webapps/community/buildapp.py", line 56, in app_factory from galaxy.webapps.community.app import UniverseApplication File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/webapps/community/app.py", line 2, in <module> from galaxy import tools File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/tools/__init__.py", line 36, in <module> import galaxy.util.shed_util_common File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/shed_util_common.py", line 27, in <module> eggs.require( 'markupsafe' ) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 413, in require return pkg_resources.working_set.require( req_str ) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/pkg_resources.py", line 666, in require needed = self.resolve(parse_requirements(requirements)) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here DistributionNotFound: markupsafe Removing PID file community_webapp.pid Should this work under Mac OS X? I suspect there are some eggs missing on the Galaxy site which would be needed: $ python2.6 ./scripts/fetch_eggs.py Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: ssh (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Regards, Peter

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sort the list of users while impersonating a user.
by Luobin Yang 31 Jan '13

31 Jan '13

Hi, The list of users is not sorted when I try to impersonate a user, this is very inconvenient because of the large number of users in the system, is there a quick way to have users sorted ? Thanks, Luobin

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patch for workflow api
by Richard Park 31 Jan '13

31 Jan '13

Hi Guys, I've just updated to the latest galaxy-central and notice a problem when trying to export workflows via the api. In galaxy-central/lib/webapps/galaxy/api/workflows.py, I just need to add in an extra tab in lines 88 and 89, the patch is below. #### PATCH #### using hg diff diff -r 43fa4cb72e0f lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 13:49:43 2013 -0500 +++ b/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 14:43:46 2013 -0500 @@ -85,8 +85,8 @@ 'type': step.type, 'tool_id': step.tool_id, 'input_steps': {}} - for conn in step.input_connections: - steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, + for conn in step.input_connections: + steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, 'step_output': conn.output_name} item['steps'] = steps return item Could someone add this simple fix? I'd really appreciate it. Please let me know if I should be submtting a patch or pull request somewhere else. thanks, Richard

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