November 2013 - galaxy-dev - lists.galaxyproject.org

Interacting with output views in Galaxy
by Stephen Taylor 04 Dec '13

04 Dec '13

Hi, I was wondering, if anyone could point me to any resources and that allow the user to interact with the view of the output of a tool in Galaxy. So for example, I would like to load an image, draw a region of interest (ROI) (probably via some js routine) and then store that information in a file, generating an input in the History view. This input could then be used for further analysis. I guess Trackster does something like this, but I don't know if its routines are generic enough to handle this type of interaction. Thanks for any info! Steve

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tiff files in galaxy
by Robert Baertsch 03 Dec '13

03 Dec '13

Do you know a fast way to open large tiff files in galaxy ? The sniffer recognizes the type, but clicking on the eyeball on a large 82mb file just hangs. Downloading the file and opening in preview does work but it is clunky. Perhaps storing a low res version that would be display when clicking the eyeball would speed access.

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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

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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

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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

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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

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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

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character set encoding metadata
by Robert Baertsch 28 Nov '13

28 Nov '13

Does galaxy have an official place to store the character set for a text file? I'm thinking of modifying the upload tool to prompt for the character set, since it cannot be sniffed. It should go in the hda/ldda metadata hash or extended_metadata for the dataset. Any opinions? BTW: everyone should watch this talk on unicode. http://bit.ly/unipain

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Re: [galaxy-dev] galaxy-dev Digest, Vol 89, Issue 32
by Dooley, Damion 28 Nov '13

28 Nov '13

Hi folks, Has someone seen this behaviour? I'm trying to do a once-over maintenance cleanup of our galaxy installs. The galaxy account is getting emailed nightly with an error which is happening when it gets to delete_datasets.sh cron task, basically: AttributeError: 'NoneType' object has no attribute 'dataset_id' 1) Now I found this thread: http://dev.list.galaxyproject.org/Error-when-running-cleanup-datasets-py-td… - and implemented that solution which removed some of the preceding log error info, but this related error remains: sh ... /production2/galaxy-dist/scripts/cleanup_datasets/delete_datasets.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in <module> if __name__ == "__main__": main() File "./scripts/cleanup_datasets/cleanup_datasets.py", line 126, in main delete_datasets( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 301, in delete_datasets dataset_ids.append( ldda.dataset_id ) AttributeError: 'NoneType' object has no attribute 'dataset_id' In the delete_datasets.log it shows that this is last log line before error occurs: ######### Processing LibraryDataset id: 14201 2) So to recap, in step 1 I found: galaxydb_prod2=> select * from library_dataset where library_dataset_dataset_association_id is null; id | library_dataset_dataset_association_id | folder_id | order_id | create_time | update_time | name | info | deleted | purged -------+----------------------------------------+-----------+----------+----------------------------+----------------------------+---------------+------+---------+-------- 14201 | | 544 | 18 | 2012-11-01 17:26:23.877817 | 2012-11-01 17:26:35.787611 | NC_006625.fna | | f | f (1 row) And so I ran the recommended query, "update library_dataset set folder_id = null where id=14201;" and that seemed to have a positive effect. For what its worth, galaxydb_prod2=> select * from library_dataset_dataset_association where id = 14201 galaxydb_prod2-> ; id | library_dataset_id | dataset_id | create_time | update_time | copied_from_history_dataset_association_id | copied_from_library_dataset_dataset_association_id | name | info | blurb | peek | extension | metadata | parent_id | designation | deleted | visible | user_id | message | state | tool_version -------+--------------------+------------+----------------------------+--------------------------+--------------------------------------------+----------------------------------------------------+---------------+------+-------+------+-----------+------------------+-----------+-------------+---------+---------+---------+---------+-------+-------------- 14201 | 14201 | 14706 | 2012-11-01 17:26:28.593081 | 2012-11-01 17:26:30.8649 | | | NC_006625.fna | | | | auto | {"dbkey": ["?"]} | | | f | t | 1 | | | (1 row) The last thing I'd say is that this 'NC_006625.fna' item doesn't show up in the website front-end's sole Data Library list of folders and sub-items, nor does it show in the deleted list. It seems orphaned but I'd rather someone had confident advice on this one. My novice attempt at surgery would probably lead to lots of blood on the table. Help much appreciated! Damion

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Active Directory
by Alexander Kurze 28 Nov '13

28 Nov '13

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?

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