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

blend4j
by Marc Logghe 03 Mar '13

03 Mar '13

Hi all, Is this the correct forum to post blend4j issues ? Apologies if this is not the case. I was trying to run a custom workflow via blend4j, according to https://github.com/jmchilton/blend4j In my hands, the call to workflowDetails.getInputs() returns an empty Map. I believe the corresponding REST request looks like: /galaxy/api/workflows/<workflow id>?key=<API key> In the JSON response, the 'inputs' attribute is empty indeed ({"url": "/galaxy/api/workflows/f09437b8822035f7", "inputs": {}, ...). I do not understand why this is the case because 2 steps require inputs to be set at runtime. Via the Galaxy web interface those required parameters can be set and the workflow is running smoothly. Or has the term 'inputs' nothing to do with 'parameters' ? Regards, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________

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Public ToolShed Problem - Latest Version isn't the tip repo
by Fei-Yang Jen 01 Mar '13

01 Mar '13

Hi Galaxy_dev team, I have question with regards to public ToolShed. For some reason, the latest version of my tools didn't get picked as tip repo when I was trying to install it on my cloud instance. I have read about some unexpected behaviours of public ToolShed if I use it like a git repo. Without knowing that at the first place, I had been modifying my tools on public ToolShed and had multiple uploads of some files. Is it possible that this is the reason why the latest version of my upload doesn't get picked as a tip repo? If it is so, how can I go about to fix it ? (I was looking for a way to delete repositories, but there didn't seem to have one) Thanks, Fei-Yang (Arthur) Jen Student Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca<http://www.oicr.on.ca> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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macs error for chipseq data
by Jennifer Jackson 01 Mar '13

01 Mar '13

Hi Kathryn, I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility. Thanks! Jen Galaxy team On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote: > > Hi Jen, > > Sorry that I missed some part of your email. It is not for local > galaxy install. I am using the cloudman from aws and it seemed to have > everything for having the input files and reference genome chose. The > job was shown on the right panel and then the error message coming out. > > It seems to me that MACS was installed.... What is the issue? > > Thank you very much, > > Kathryn > On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: > > Hi Jennifer, > > Thanks for the information on MACS tools. > > Yes, I forgot to mention that I used bowtie mapped files as the input. > > Thank you very much, > > Kathryn > > ** > > *From:*Jennifer Jackson [mailto:jen@bx.psu.edu] > *Sent:* Friday, January 11, 2013 3:48 AM > *To:* Sun, Wenping [USA] > *Cc:* galaxy-user(a)bx.psu.edu > *Subject:* [External] Re: [galaxy-user] macs error for chipseq data > > Hello Kathryn, > > This is occurring on your local Galaxy install? Have you installed the > actual MACS tool and set up the proper configuration paths? Details > for how to do this are in these wikis: > http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies > http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies > > Apart from that, I should let you know that prior to running MACS, > groomed fastq datasets first need to be mapped. An example can be > found in our Using Galaxy paper, protocol #3. Links to the paper and > supplemental materials (including a screencast walk-through) are > available here: > https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 > > If you need more help with your local install, directing questions to > the galaxy-dev(a)bx.psu.edu <mailto:galaxy-dev@bx.psu.edu> mailing list > would be best, > > Thanks! > > Jen > Galaxy team > > On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: > > Dear galaxy users, > > I've encountered the error while running macs on galaxy for > chipseq data. I used fastq groomed files as input and had the > following error > > An error occurred running this job: //bin/sh: macs: not found/ > > // > > Anybody can kindly provide some hints? > > Thanks, > > Kathryn > > > > > ___________________________________________________________ > > The Galaxy User list should be used for the discussion of > > Galaxy analysis and other features on the public server > > at usegalaxy.org. Please keep all replies on the list by > > using "reply all" in your mail client. For discussion of > > local Galaxy instances and the Galaxy source code, please > > use the Galaxy Development list: > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > To manage your subscriptions to this and other Galaxy lists, > > please use the interface at: > > > > http://lists.bx.psu.edu/ > > > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Problem installing Deseq from toolshed
by Mahtab Mirmomeni 01 Mar '13

01 Mar '13

Hi all, I have installed Deseq (by vipints) from the main galaxy toolshed and have followed the make instructions but I'm still not unable to run it inside Galaxy and I get the following error. (Path is the path to our local galaxy instance) error: get_read_counts: Path/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076…: failed to load: /mnt/all/cloudman/galaxy/clare/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076/deseq_hts/deseq-hts_1.0/mex/get_reads.mex: undefined symbol: bam_index_destroy error: called from: error: Path/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076… at line 97, column 34 starting Octave failed I should add that I can run octave from command line and it seems to be working. Any suggestions is much appreciated. Thanks Mahtab

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Re: [galaxy-dev] all the data files in .loc files needed to download ?
by Carl Eberhard 01 Mar '13

01 Mar '13

Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn <shenwiyn(a)foxmail.com> wrote: > ** > Hi Carl Eberhard, > Thank you very much for you help.I have another some questions : > First, > we need to install the needed data,for example sam_fa_indices.loc file of > SAM Tools : > index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1. > fa > index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3. > fa > index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ > ailMel1.fa > index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/ > anoCar2.fa > index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/ > apiMel2.fa > index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/ > apiMel3.fa > index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/ > aplCal1.fa > .... > so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2. > fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx. > psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? > Second, > from the needed datas mentioned in the .loc files in > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to > download too much data,can we get all these data from some website instead > of searching them on Iternet one by one? > > > Thanks, > shenwiyn > > > > ------------------------------ > > *From:* Carl Eberhard <carlfeberhard(a)gmail.com> > *Date:* 2013-02-22 01:20 > *To:* shenwiyn <shenwiyn(a)gmail.com> > *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to > download ? > Hello, > Yes a local galaxy requires a few steps in order to install the needed > data. > > The following wiki page should help get you started: > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup > > Let me know if you need more information, > Carl > > > > On Tue, Feb 19, 2013 at 3:59 AM, shenwiyn <shenwiyn(a)gmail.com> wrote: > >> ** >> Hi all, >> Are all the data files in .loc files needed to download and put to the right directory when >> we install our local galaxy? >> >> thaks >> shenwiyn >> >> ------------------------------ >> shenwiyn >> >> ___________________________________________________________ >> 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/ >> > >

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first install, MySQL date
by Arnau Bria 01 Mar '13

01 Mar '13

Hi all, my name is Arnau Bria and I work at CRG, in BCN. I'm a sysadmin and I'm helping one user to install/configure galaxy and to run jobs in our SGE cluster. I think this is the correct list for asking SGE/MySQL questions, if not, let me apology in advance. I have a question about MySQL dates. system date is correct and uses CET (I'm in Spain), MySQL i sconfigured to use system's timezone: date Thu Feb 28 13:38:10 CET 2013 SELECT @@global.time_zone, @@session.time_zone; +--------------------+---------------------+ | @@global.time_zone | @@session.time_zone | +--------------------+---------------------+ | SYSTEM | SYSTEM | +--------------------+---------------------+ 1 row in set (0.02 sec) but SGE job dates are wrong: create_time 2013-02-28 12:37:48 notice it shows 12:37 and it should be 13:37. is this importatn? may I change glaxy's timezone in some way? TIA, Arnau

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bowtie-wrapper
by Alexander Kurze 28 Feb '13

28 Feb '13

Hello, I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads? If I use bowtie vi comman line I get following output: > bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s) The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy. Any idea how I can still access the stats? Thanks, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341

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purging datasets doesn't free up disk space
by Sarah Diehl 28 Feb '13

28 Feb '13

Hello, our Galaxy server is running low on disk space, so I asked all users to (permanently) delete old histories and datasets. One specific user alone managed to reduce his space usage by 2 TB. That's at least what the Galaxy server says. Afterwards I additionally ran the following scripts: delete_userless_histories.sh -d 1 -r -f purge_histories.sh -d 1 -r -f purge_libraries.sh -d 1 -r -f purge_folders.sh -d 1 -r -f python cleanup_datasets.py universe_wsgi.ini -d 200 -6 -r -f purge_datasets.sh -d 1 -r -f Purging the histories took very long (about a day) and the log of deleted histories is huge. Purging the datasets also took some time. However, my disk usage is still the same as before. It wasn't reduced at all. Did I miss some important step or some waiting time? Any help would be appreciated. Thanks, Sarah

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access to api when using apache ldap auth
by Langhorst, Brad 28 Feb '13

28 Feb '13

I need to access the api using an api key… Does anybody have a working apache configuration for that? A search at galaxyproject.org/search<http://galaxyproject.org/search> didn't turn anything up. I tried this: but that causes the history to fail to update. <Location "/"> Order allow,deny allow from all AuthType Basic AuthName "NEB Credentials" AuthBasicProvider ldap AuthzLDAPAuthoritative off AuthLDAPBindDN xxxx@yyyy AuthLDAPBindPassword xxxxx AuthLDAPURL "ldap://<host…>?sAMAccountName" require valid-user RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary XSendFile on XSendFileAllowAbove on </Location> <Location "/api"> Satisfy Any Allow from all </Location> I must keep that /api location commented out for history updates to work. If i uncomment it, i can use the api. What's the right solution? Maybe i should add a /api2 alias that does not require valid-user? Maybe my apache foo is just too weak and I'm missing something obvious? Thanks for any advice! Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com>

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Macs14 - Invalid Literal for int error
by greg 28 Feb '13

28 Feb '13

Hi guys, (Sorry for showing up on this list so much, hopefully I'll get everything running soon!) On our local galaxy install when I try to run MACS14 like this: http://snag.gy/RYBBN.jpg we get this error: Dataset generation errors Dataset 74: MACS14 on data 29 and data 24 (peaks: bed) Tool execution generated the following error message: Traceback (most recent call last): File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 132, in <module> if __name__ == "__main__": main() File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 94, in main xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' ) File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 40, in xls_to_interval fields[1] = str( int( fields[1] ) - 1 ) ValueError: invalid literal for int() with base 10: 'start'

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