- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] [Galaxy-ZBIT] Help needed in Galaxy Uploading files.
by El-Sayed Hegazy 03 Dec '13

03 Dec '13

Dear Dr Johannes,Alot of thanks for you but i already sent the same issue to galaxy-dev(a)lists.bx.psu.edu the galaxy mailing list without reply i am so sorry for disturbance Best Regards, https://www.mcpvirtualbusinesscard.com/VBCServer/elsayedhegazy/interactivec… HegazyIT Manager at ALHAYAH LabsBioinformatician - Software developer Mobile: +2 0100 6 99 88 36e-mail: elsayedhegazy(a)live.com > Date: Tue, 3 Dec 2013 10:15:22 +0100 > From: johannes.eichner(a)uni-tuebingen.de > To: elsayedhegazy(a)live.com > CC: andraeger(a)eng.ucsd.edu > Subject: Re: [Galaxy-ZBIT] Help needed in Galaxy Uploading files. > > Dear Mr. Hegazy, > > please note that we only provide support for the customized Galaxy > instance hosted at http://webservices.cs.uni-tuebingen.de. > > If you have any questions considering the main Galaxy instance which > also offers the NGS TOOLBOX BETA (https://usegalaxy.org) please contact > the core development team by joining the galaxy mailing list > (galaxy-dev(a)lists.bx.psu.edu) as described here: > http://wiki.galaxyproject.org/MailingLists#Posting_a_Question > > Kind regards, > Johannes > > > On 12/03/2013 08:37 AM, El-Sayed Hegazy wrote: > > Dear Dr Andreas,When i using Galaxy website and then go to Analyze data section and navigate through tools i found NGS tool box used for Next Generation Sequencing data analysis from Quality control like Groomer and trimming and filtering and then we can make mapping and more with Illumina RAW data files Its actually part of Galaxy services Called NGS tool box Beta > > I need to clarify what i miss ? > > Alot of thanks for you > > Best Regards, > > https://www.mcpvirtualbusinesscard.com/VBCServer/elsayedhegazy/interactivec… HegazyIT Manager at ALHAYAH LabsBioinformatician - Software developer Mobile: +2 0100 6 99 88 36e-mail: elsayedhegazy(a)live.com > > > >> Date: Mon, 2 Dec 2013 09:28:10 -0800 > >> From: andraeger(a)eng.ucsd.edu > >> To: elsayedhegazy(a)live.com; galaxy(a)listserv.uni-tuebingen.de > >> CC: mahef111(a)gmail.com > >> Subject: Re: [Galaxy-ZBIT] Help needed in Galaxy Uploading files. > >> > >> Dear El-Sayed Hegazy, > >> > >> Due to the long Thanksgiving weekend I could not reply to you earlier. > >> Thank you for your patience. I now downloaded your file and had a look > >> into it. What I realized from your e-mail is that you are interested in > >> next generation sequencing, NGS, which is actually not part of our > >> services. We do not provide any tools that facilitate handling this kind > >> of data. So, I would like to know what you intended to do with your > >> file; i.e., to which tool did you like to upload it and what was your > >> envisaged analysis? > >> > >> Thanks > >> > >> -- > >> Dr. Andreas Draeger > >> University of California, San Diego, La Jolla, CA 92093-0412, USA > >> Bioengineering Dept., Systems Biology Research Group, Office #2506 > >> Phone: +1-858-534-9717, Fax: +1-858-822-3120, twitter: @dr_drae > >> > > > > > > > > > > _______________________________________________ > > Galaxy mailing list > > Galaxy(a)listserv.uni-tuebingen.de > > https://listserv.uni-tuebingen.de/mailman/listinfo/galaxy > >

1 0

survey
by Philippe Moncuquet 03 Dec '13

03 Dec '13

Hi, I hope this is relevant to the dev list but if it is not please let me know. I was trying to estimate active users out of our registered users. I ended counting users that had a job during the last month. How would you guys do ? During this process I also wanted to see how we were doing in comparison to other instance. I set up a simple survey and would greatly appreciate if instance admin would take 2 min to complete it. I will publish results here (or maybe to some more relevant place, let me know) at the end of the month. https://fr.surveymonkey.com/s/CD6NN88 Regards, Philip

3 2

Subclassing downloadable archive file for composite datatypes
by Peter Cock 02 Dec '13

02 Dec '13

Hello all, I would like to modify the default ZIP bundle behaviour for composite datatypes, which currently insists on creating an HTML "main" file. To do this I think the current monolithic _archive_composite_dataset function needs to be refactored in file lib/galaxy/datatypes/data.py I would like to move the section which currently names and populates the HTML index file into a sub-method, i.e. this chunk: path = data.file_name fname = os.path.split(path)[-1] efp = data.extra_files_path htmlname = os.path.splitext(outfname)[0] if not htmlname.endswith(ext): htmlname = '%s_%s' % (htmlname,ext) archname = '%s.html' % htmlname # fake the real nature of the html file try: archive.add(data.file_name,archname) except IOError: error = True log.exception( "Unable to add composite parent %s to temporary library download archive" % data.file_name) msg = "Unable to create archive for download, please report this error" Then by overriding this new method a subclass (custom composite datatype) could for example set the filename used inside the archive to be "index.html" or "index.htm" or anything else like "README.txt" (doesn't have to be HTML); alter the contents of the index file; or even not include an index file in the archive. Would a pull request to do this be considered? Thanks, Peter

2 7

job_conf.xml output_size limit
by Sarah Diehl 02 Dec '13

02 Dec '13

Hi everyone, in my job_conf.xml I defined the following limit <limit type="output_size">536870912000</limit> Galaxy seems to correctly identify the number as 500 GB, since I got the error: "Job output file grew too large (greater than 500.0 GB), please try different inputs or parameters" The problem is that the output file of the job is just a few GB (verified by rerunning the command manually). So Galaxy is wrongly stopping the job after just a few seconds, although the actual output size was fine. I disabled the limit for now, but I really want it in place. I just put it because I had a user generating output files of over 4 TB that filled up our storage (quotas only catch them when they are finished, but the user had two concurrent jobs running, both creating such huge files). Any help is appreciated! Thanks! Sarah

1 0

December 2013 Galaxy Update
by Dave Clements 02 Dec '13

02 Dec '13

1 0

Error running Clustalw and HyPhy on Cloudman
by Karen Miga 01 Dec '13

01 Dec '13

Hello - I am running to errors when trying to run Clustalw and HyPhy on our cloudman instance. (1) Clustalw: The program completes without error and produces an empty file and a log file that states "/bin/sh: 1: clustalw2: not found" Searching around a bit I am not seeing clustalw2 previously installed. I am happy to do it if need be, however, I wanted to check in and see if I am overlooking the directory or an easy fix. If I do need to install clustalw, I would prefer to use clustalw-omega, but was not sure if I needed to script a brand new wrapper or if I could use the previous one that came with galaxy image. (2) HyPhy: The cloud the link was initially broken. I changed it to the correct path: sudo ln -sfn /mnt/galaxy/tools/hyphy/default /mnt/galaxy/galaxy-app/tool-data/HYPHY I am using a fasta alignment file of 6 protein sequences (566 AA each) as a test case (*also fails with nucleotide alignments). It runs briefly and then issues an error statement "Single Alignment Analyses Segmentation fault (core dumped)". Thank you in advance, Karen

3 10

Re: [galaxy-dev] Active Directory
by Stewart, Andrew 01 Dec '13

01 Dec '13

Hi Alex, I've been trying to do something similar. There are no doubt others on this list who can offer more official answers than mine, but I'm happy to share my experience so far: 1) First of all, do make sure to read through http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer. It's the best starting point for customizing your local production deployment. 2) For AD authentication, it is indeed possible to kick that off to the Apache proxy to handle. I ended up opting out of using it because of some anomalies and my lack of AD knowledge, and frankly I think there are some UX disadvantages to using apache's generic authentication prompt. Personally I'd like to see AD or other authentication handling be served directly by the Galaxy backend (same login prompt and everything), but that's just my personal taste. Applicable documentation: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy 3) I think there are a couple ways to go about this, but none of them are direct. Actually mounting the shares will probably be the most difficult part, especially if you need to take permissions into account. On the AD side, you'll want to first verify that the shared drive is mountable by the OS of your Galaxy server. Depending on how the share is configured (AD file permissions vs linux file permissions), you might have some trouble matching permissions on, say, a linux server. Assuming you can mount to your Galaxy server, I personally think the easiest thing to do would be to mount not individual user shares but rather a single share with individual user directories. You could potentially take advantage of Galaxy's FTP Upload functionality (http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP) at this point, sans the ftp server. Let's say you mounted the AD governed single point share to /mnt/ad-drive. You could set 'ftp_upload_dir=/mnt/ad-drive' in Galaxy's universe_wsgi.ini file. The trick here would be to get Galaxy to map user directories under /mnt/ad-drive in a manner that Galaxy's FTP interface understands. To do it Galaxy's way, you would want user directories to appear as their full e-mail address as registered with Galaxy; so, for example "alexander.kurze(a)bioch.ox.ac.uk" would appear on the share as literally "/mnt/ad-drive/alexander.kurze(a)bioch.ox.ac.uk". The fact that users would be registering on galaxy with their AD credentials would help keep that system in sync. With the ftp_upload_dir option configured, user(a)bioch.ox.ac.uk would see an extra option in the Import Data interface to directly import data files from /mnt/ad-drive/user(a)bioch.ox.ac.uk. As far as exporting data from their Galaxy account to the shared drive, I've come across a couple tools in the Galaxy ToolShed that do exactly that. Alternatively, I don't know if your server is sitting in front of a cluster, but you could always go down the route of running jobs as the actual system user, assuming a system configuration where system users are AD users. See: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster Hope some of that is helpful. -- Andrew Stewart Office of Research Information Services (ORIS), Office of the Chief Information Officer (OCIO), Smithsonian Institution 202-505-3633 On 12/1/13 12:00 PM, "galaxy-dev-request(a)lists.bx.psu.edu" <galaxy-dev-request(a)lists.bx.psu.edu> wrote: >Message: 1 >Date: Thu, 28 Nov 2013 14:06:58 +0000 >From: Alexander Kurze <alexander.kurze(a)bioch.ox.ac.uk> >To: galaxy-dev <galaxy-dev(a)bx.psu.edu> >Subject: [galaxy-dev] Active Directory >Message-ID: > <CABaBi0cTcQvDfLwJ2WLJG0FDBkWD2LALnEs6yRqFVwFya5K=Rw(a)mail.gmail.com> >Content-Type: text/plain; charset="iso-8859-1" > >Hi there, > >I have a server set up of galaxy. I would like to have a system setup >where >people can login via their active directory name and then use their >mounted >share drive to download processed data from the galaxy server. > >I saw that it is possible via apache to login through the AD, but will the >AD also mount the share drives? If yes, is there a wrapper that allows to >download Galaxy Histories onto the shared drive? > >Alex

1 0

Patch for lib/galaxy/webapps/galaxy/api/provenance.py for optional dataset parameters
by Jim Johnson 30 Nov '13

30 Nov '13

lib/galaxy/webapps/galaxy/api/provenance.py throws an exception when an optional dataset parameter is None Traceback (most recent call last): File "/Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py", line 199, in decorator rval = func( self, trans, *args, **kwargs) File "/Users/jj/gxt/gxt/lib/galaxy/webapps/galaxy/api/provenance.py", line 18, in index value = self._get_provenance( trans, self.provenance_item_class, kwd[self.provenance_item_id], follow ) File "/Users/jj/gxt/gxt/lib/galaxy/webapps/galaxy/api/provenance.py", line 38, in _get_provenance out = self._get_record(trans, provenance_item, follow) File "/Users/jj/gxt/gxt/lib/galaxy/webapps/galaxy/api/provenance.py", line 50, in _get_record "parameters": self._get_job_record(trans, job, follow), File "/Users/jj/gxt/gxt/lib/galaxy/webapps/galaxy/api/provenance.py", line 65, in _get_job_record "id": trans.security.encode_id(in_d.dataset.id), AttributeError: 'NoneType' object has no attribute 'id' $ hg diff lib/galaxy/webapps/galaxy/api/provenance.py diff -r 228156daa575 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py Fri Nov 29 17:06:02 2013 -0500 +++ b/lib/galaxy/webapps/galaxy/api/provenance.py Sat Nov 30 08:08:56 2013 -0600 @@ -58,6 +58,8 @@ for p in job.parameters: out[p.name] = p.value for in_d in job.input_datasets: + if not in_d.dataset: + continue if follow: out[in_d.name] = self._get_record(trans, in_d.dataset, follow) else: -- James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota

2 1

Tool never get properly installed into Galaxy
by Stephanie LE GRAS 29 Nov '13

29 Nov '13

Dear Galaxy community, I'm facing a problem in installing a tool from the tool-shed repository for a while now and I still don't know how to make it. I'm trying to install deepTools (https://github.com/fidelram/deepTools) into our Galaxy instance but I never got the tools neither properly installed nor working. To make a long story short : I installed deepTools from the admin panel but got an error due to one of the dependencies (Scipy). I solved the dependency problem, uninstalled the tool and try to reinstall it. When I tried to reinstall the tool, nothing happened in the panel "monitor installing tool shed repositories". And when I look at what's is prompted from Galaxy logs. The same message is prompted again and again until I leave the "monitor installing tool shed repositories" page (see attached file). I also tried to reinstall the tool from the API but I've been told that I cannot since the tool has already been previously installed. Is there a way to completely remove a tool from Galaxy to restart the tool installation from the beginning? Thank you in advance for your help, Stephanie -- Stephanie Le Gras INSERM Computational scientist - Bioinformatician Microarray and high throughput sequencing platform IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73

2 2

Missing test results on (Test) Tool Shed
by Peter Cock 29 Nov '13

29 Nov '13

Hi Greg & Dave, I really like the new features on the (Test) Tool Shed for searching my repositories: * Latest revision missing tool tests * Latest revision failing tool tests * Latest revision all tool tests pass However there are some teething problems. Some of my tools are listed under "Latest revision failing tool tests", but when I go to look at them, no test results are shown (passing or failing): http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3 http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip In some cases there is indeed a failing test, for instance this is due to a bug in the test framework: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go https://trello.com/c/KdGX3hkh And here there are missing dependencies (due to restrictive licensing problems): http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp https://trello.com/card/-/506338ce32ae458f6d15e4b3/770 Peter

4 77