galaxy-dev December 2013

galaxy-dev@lists.galaxyproject.org

67 participants
99 discussions

Blast+: new feature filter/mask... by taxid before job in one task
by Berner, Thomas 27 Feb '14

27 Feb '14

Hi guys, We recently installed NCBI BLAST + to our local Galaxy instance and now we need to provide the possibility to filter/mask ... by taxon id (taxid) using the command line option (-window_masker_taxid) of BLAST (cf. http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the job will be performed in one task. However searching in the documentation and the mailing list, I did not find anything about this. So it would be great to provide the possibility to subselect by taxid (e.g. NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing the BLAST integration. We believe this could be of common interest. It would be great if anybody could comment on this. Thanks a lot, Thomas

3 4

Galaxy Tool Shed packages for Biopython
by Peter Cock 18 Feb '14

18 Feb '14

Hi all, I've send this to both the Galaxy and Biopython developers lists, and hope this will make sense to both groups. If you've not heard of Galaxy, start here: http://galaxyproject.org - while the easy to guess Biopython website is at http://biopython.org Brad Chapman and I are both Biopython core developers, and are also both on the "IUC" Galaxy Tool Shed committee because we've been quite involved in wrapping and writing tools for use on Galaxy. Fellow committee member Björn Grüning has done a lot of the hands on work defining package definitions for dependencies within the Galaxy Tool Shed ecosystem - including defining them for Biopython, NumPy, SciPy, MatPlotLib, etc. We're very grateful for his hard work - most of which is now available under the IUC group account: http://toolshed.g2.bx.psu.edu/view/iuc/ http://testtoolshed.g2.bx.psu.edu/view/iuc/ The Biopython packages, however, are under a dedicated "biopython" account on the Galaxy Tool Shed to which currently Bjoern, Brad and I have access to: http://toolshed.g2.bx.psu.edu/view/biopython/ http://testtoolshed.g2.bx.psu.edu/view/biopython/ This packaging work was initially tracked in Bjoern's own GitHub repository, https://github.com/bgruening/galaxytools/ We (me, Brad and Bjoern) agreed that a Biopython owned repository would be more sensible in the long term, so I have created this and ported Bjoern's commits to it: https://github.com/biopython/galaxy_packages Currently the "Galaxy packagers" team on GitHub which has read and write access to this new repository is just me, Brad and Bjoern. Regards, Peter

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shed tool dependencies
by Geert Vandeweyer 14 Feb '14

14 Feb '14

Hi, Is there a default notation to specify perl modules (threading modules) in a tool configuration or in a submission to the toolshed? I've got some tools to share that make extensive use of these modules, and they are not default in a perl distribution. Hence, I'd like to inform the users that they need to install these modules (or that they get installed by the the toolshed using cpan ?) Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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Several jobs stalled in the queue: Job runner assigned but no external ID recorded
by Derrick Lin 05 Feb '14

05 Feb '14

Hi guys, I have several jobs have been stuck in the queue for long time, I checked the handler log and found the following message: Job runner assigned but no external ID recorded, adding to the job handler queue Is there a way that I can clean these orphan jobs out of the queue? Cheers, Derrick

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A new tool_data_table_conf.xml created under tool-data directory
by Derrick Lin 17 Jan '14

17 Jan '14

Hi guys, After installing the BWA from the Tools Shed, I find there is a new tool_data_table_conf.xml got created under tool-data directory. The file contains the entries of BWA's loc files. I believe the installed BWA still relies on the tool_data_table_conf.xml under galaxy root dir. Anyone can clarify what the one under tool-data dir is for? Regards, Derrick

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trackster error for viewing rat data (rn5)
by Shu-Yi Su 13 Jan '14

13 Jan '14

Hi, I am trying to view rat data (rn5) using trackster with data format bam or bigwig on our galaxy installation, but it isn't working. It works with other organisms, such as dm3 or hg19. There is error message in the log: 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] "GET /galaxy-dev/api/genomes/rn5?low=0&num=100 HTTP/1.1" 200 - "http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc71049…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1" 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] "GET /galaxy-dev/api/datasets/83c20bbc7104922b?hda_ldda=hda&data_type=track_config HTTP/1.1" 200 - "http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc71049…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1" galaxy.webapps.galaxy.api.datasets ERROR 2013-11-20 16:14:21,795 Error in dataset API at listing contents: 'BinaryFileReader' object has no attribute 'read_bits64': 'BinaryFileReader' object has no attribute 'read_bits64' Traceback (most recent call last): File "/g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py", line 44, in show is_true( kwd.get( 'retry', False ) ) ) File "/g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py", line 106, in _converted_datasets_state if not data_provider.has_data( chrom ): File "/g/funcgen/galaxy-dev/lib/galaxy/visualization/data_providers/genome.py", line 1078, in has_data all_dat = bbi.query( chrom, 0, 2147483647, 1 ) or \ File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) File "bbi_file.pyx", line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' I also attached the first few lines in our rn5.len: chr1 290094216 chr2 285068071 chr4 248343840 chr3 183740530 chr5 177180328 chr6 156897508 chrX 154597545 chr7 143501887 chr8 132457389 chr9 121549591 chr13 118718031 chr14 115151701 chr15 114627140 chr10 112200500 chr11 93518069 chr17 92503511 chr16 90051983 chr18 87229863 chr19 72914587 chr20 57791882 chr12 54450796 chr4_AABR06109730_random 227955 chrUn_JH620568 73090 chr2_JH620298_random 62026 chr5_JH620330_random 58807 chrUn_JH620520 57992 chrUn_JH620553 56877 chr1_AABR06109393_random 52834 chr18_JH620420_random 51685 chr9_JH620364_random 51490 chrX_JH620445_random 49212 chrUn_JH620623 47760 chr10_JH620371_random 44089 I have looked into this error for a while and still can't figure it out. Any idea or suggestions are very appreciated. Thank you very much. Best regards, Shu-Yi

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repository metadata reset not always working
by Lukasse, Pieter 10 Jan '14

10 Jan '14

Hi Greg, I found an issue in Toolshed, not sure if it has been reported before. Steps: 1- Make a repository and add a tool .xml and a README file 2- Reset metadata and check if all information appears in the toolshed UI 3- Now delete the README file from the hg repository 4- Commit 5- (not sure whether I did this step) reset metadata 6- Now add the README file back but with different contents. Commit, reset metadata 7- In the toolshed UI you will see that the OLD REAME contents are displayed. This is just one example...I have the feeling it is not restricted to the README files of course...so it can be quite a serious issue. Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Cloud Launch - Where is /mnt/galaxyData
by greg 07 Jan '14

07 Jan '14

Hi guys, I just launched an instance from https://usegalaxy.org/cloudlaunch and chose "data cluster" when prompted. Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData Background: Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers. I did this successfully a year or two ago by installing it to /mnt/galaxyData. Thanks, Greg

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Is there a way yet to more easily determine name of inputs for renaming in workflows
by Thon deBoer 03 Jan '14

03 Jan '14

Hi, In order to make Galaxy workflows even more useful, it is going to be important for data files to be renamed in a workflow. I know we can use the "#{input1 | base name}-BWA.sam" trick which is useful IF you know what the actual parameter name is in the XML file. There was some discussions some years ago (http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011288.html) but it is is now very time consuming to figure out from the XML file what the name of the input parameter is you would like to use (and it is often very tricky, due to the fact that the name of the actual input parameter may actually change based on some selection in the UI…. I often had to resort to actually chaining the XML file to make the output something like: <data format="sam" name="output" label="#echo os.path.splitext ( str ( $paired.input1.name ).replace ( '_R1' , '' )) [ 0 ]#-bwa_#echo str ( $paired.sPaired ) #.sam”> But that is time consuming and does no longer work with the toolshed since an update of a tool is merely a brute force replacement of the previous version, no longer allowing me to have to change it once and let the updates work with on the changed version as was working brilliantly before all tools were moved out of the main branch and into the toolshed)… So, are there any plans to at least expose the Inputs (or the XML) during the workflow editing or something similar? Now I have to dig up the XML file every time I use a new tool, making the creation of workflow a tedious task... Regards, Thon [cid:enz_logo_2_newf03327] Thon deBoer Director of Software 3415 Colorado Ave. Room A255 Boulder, CO 80303 Cell: (650) 799-6839 tdeboer(a)enzymatics.com www.enzymatics.com Enzymatics Inc. Confidentiality Notice: This e-mail and any attachments are confidential, proprietary and or privileged information. It is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone other than the intended recipient(s). If you are not an intended recipient, please delete this e-mail immediately and notify the sender by e-mail.

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Uploading gzipped fastq files through the API
by dsobral＠igc.gulbenkian.pt 03 Jan '14

03 Jan '14

Hello, I have been using the galaxy API to upload files into a library (using a local folder for library import) and running a workflow into a history. I have been following the example scripts that come with galaxy. When I upload a gzipped fastq file, in autodetection mode (linking the file and not copying, to be faster), the file is not detected as fastq. Even if I explicitly say that it is a fastq, the file is uploaded as a fastq but with its contents gzipped (so downstream analysis fail). Nonetheless, if I do this manually through the interface, the file is unzipped correctly. Any idea how can I upload the gzipped fastq through the API so that it can be used properly? Thank you. ===================================== Daniel Sobral Next Generation Sequencing Data Analyst IGC - Instituto Gulbenkian de Ciencias e-mail dsobral(a)igc.gulbenkian.pt =====================================

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galaxy-dev December 2013