- galaxy-dev - lists.galaxyproject.org

Status of GATK in Galaxy
by Bjoern Gruening 21 Nov '13

21 Nov '13

Hi, I found that the GATK tools do not have the same requirement tag. For example indel-realigner has version 1.4, realigner_target_creator has version 1.3. Is that correct? What is the recent version that is required for GATK? Also realigner_target_creator uses the "gatk_picard_indexes" location file, but under tool-data is only a gatk_sorted_picard_indexes.loc file. Are there any concrete plans for the GATK wrappers. Especially to update to a newer version. Or is that not feasible because of this complicated license policy and the phone-home option ... I found the following trello card, but its a little bit outdated: https://trello.com/c/IPkT2spd Is anyone running a recent GATK version in Galaxy? Thanks! Bjoern

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Lock Galaxy job submission
by Peter Cock 21 Nov '13

21 Nov '13

Hello all, It is my recollection that under the "Admin" panel, "Manage jobs" page, there used to be a toggle control to lock the submission of new jobs. This was very helpful in preparation for scheduling a system shutdown (e.g. for hardware or software updates). However, I no longer see this option on either galaxy-central or galaxy-dist. Was it removed, or am I imagining things - in which case should I file an enhancement request ;) (I've had a look in Trello and didn't find anything) Thanks, Peter

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NCBI Blast+ "BLAST XML to tabular" tool question - ADDENDUM
by Dooley, Damion 20 Nov '13

20 Nov '13

Woops - I realize now findtext() must be unescaping all ">", so Peter was trying to address other non-splitting occurances of " >" as per his patch notes. But perhaps a stop_err() isn't merrited in this case? So ignore my test for ">" comment. Regards, Damion

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Samtools and idxstats
by Michiel Van Bel 20 Nov '13

20 Nov '13

Hi, I would like to inquire whether anyone has attempted to implement the idxstats tool from samtools into Galaxy? The xml-file for idxstats is not present in the Galaxy source code, which led me to try and implement it myself. However, the main problem I face is that the idxstats tool silently relies on having an index file available (within the same directory) for the bam file you which to print the stats for. E.g. samtools idxstats PATH/test.bam searches for PATH/test.bam.bai and gives an error when this file is not present. And somehow I cannot model this behavior in Galaxy. A different solution would of course be to ask the author(s) of samtools to have an option available where the user can directly indicate the path to the index file. regards, Michiel PS: I've searched the mailing list archives for this problem but did not find any matches. Apologies if I somehow missed the answer. -- ================================================================== Michiel Van Bel, PhD Expert Bioinformatician Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel(a)psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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unable to share dataset history
by Manisha Sapre 20 Nov '13

20 Nov '13

Hello Team Galaxy trying to share/ forward dataset history from user 1 ( running on a local instance,Scrn.1) to user 2 (running on cloud amazon ec2 instance,Scrn.2) and vice-versa, error:- user is not a valid galaxy user. getting this error while both the users are logged into system and both the instance's are running normal. insights of team will be very helpful. Thanks msapre [cid:EE64498E-7E1E-49C1-BD89-8AAB2EA54F11] [cid:8CB45B82-801C-4016-A17A-9FE4ED7F8C2E]

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Re: [galaxy-dev] secure Galaxy with SSL
by Jingchao Zhang 19 Nov '13

19 Nov '13

Hi Peter, Thanks so much for your help! It is like you said a browser issue. I also noticed that the Galaxy main server (https://usegalaxy.org/) doesn't have this problem. And their USCS main table browser uses "https" instead of "http". Does anyone know why this isn't included in the current Galaxy release? And how can I change my current "http USCS main" to "https USCS main"? Thanks, Jim Message: 8 Date: Tue, 19 Nov 2013 08:51:03 +0000 From: Peter Briggs <peter.briggs(a)manchester.ac.uk> To: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] secure Galaxy with SSL Message-ID: <528B2677.9050706(a)manchester.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hello Jim Re your problem #1 (UCSC browser appears to be blocked), I've seen something similar with our local Galaxy instance, which is also served via https. In our case I believe this is actually a browser issue: the latest version of Firefox silently blocks mixed secure and insecure content: https://blog.mozilla.org/tanvi/2013/04/10/mixed-content-blocking-enabled-in… (I think Chrome and IE do something similar, although IE at least gives a warning.) The workaround is either to disable mixed content blocking (not trivial in Firefox, and probably not a good idea in general), or to do something like e.g. right-click "Open link in new tab" on the "Get data"/"UCSC main table browser" link in Galaxy. Once UCSC has loaded in the new tab it can be used to send data back to Galaxy without any problems. HTH Best wishes, Peter On 18/11/13 23:03, Jingchao Zhang wrote: > Dear all, > > Today I installed the SSL module for our local Galaxy instance and the > "https://" link is working fine. I added this > "<Location"/"> > > RequestHeader set X-URL-SCHEME https > > </Location>" > in our Apache configuration file as instructed in this webpage: > http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy > > Here are my problems with SSL: > 1. Some build in links like "UCSC Main > <http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl…> table > browser" and "UCSC Test > <http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-g…> table > browser" become invalid. If I click on them, nothing will happen, as if > they are blocked. > 2. The old "http" link still works, which I think shouldn't because I > added the "RequestHeader ... https" line in Apache configuration. I > really want to disable the http link because the new users could be > easily led to the old one. > > Both httpd and Galaxy have been restarted after the changes are made. > Since I didn't find any similar threads in the mailist, I hope someone > here can help me out with this. > > Thanks, > Jim > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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wigTobigwig error: broken pipe and len file not found
by ruiwang.sz 19 Nov '13

19 Nov '13

Hi All, I‘m seeing some weird error messages...I googled but didn't see anything useful: So, it is during the wigToBigwig conversion: Dataset generation errors Dataset 47: Wig/BedGraph-to-bigWig on data 43 Tool execution generated the following error message: grep: writing output: Broken pipe grep: writing output: Broken pipe grep: writing output: Broken pipe and many more lines of the same error The tool produced the following additional output: Couldn't open tool-data/shared/ucsc/chrom/mm10.len , No such file or directory but it is there: ls -l tool-data/shared/ucsc/chrom/mm10.len -rw-rw-r-- 1 bioinfoadmin bioinfoadmin 1405 Oct 9 11:33 tool-data/shared/ucsc/chrom/mm10.len >From the Galaxy server log, I found these: galaxy.tools WARNING 2013-11-15 17:46:43,200 Failed to resolve dependency on 'ucsc_tools', ignoring galaxy.jobs.runners.local DEBUG 2013-11-15 17:46:43,255 (216) executing: grep -v "^track" /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_458.dat | wigToBigWig stdin tool-data/shared/ucsc/chrom/mm10.len /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_473.dat -blockSize=256 -itemsPerSlot=1024 -clip 2>&1 || echo "Error running wigToBigWig." >&2 and then, setmetadata set the dataset state to ERROR. I did verify that the result dataset_473.dat has a size 0. However, when I run the command alone: grep -v "^track" /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_458.dat | wigToBigWig stdin tool-data/shared/ucsc/chrom/mm10.len /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_473.dat -blockSize=256 -itemsPerSlot=1024 -clip it successfully generated the dataset_473.dat. also, I look into the wig_to_Bigwig.xml in tools/filters, the command is: grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 however, I don't see where this "$chromInfo" was defined, yet it indeed found the the correct value: tool-data/shared/ucsc/chrom/mm10.len. how does that happen? it is very puzzling...I'm not sure if anyone has seen this before, please let me know! Thanks, Rui

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Next GalaxyAdmins Meetup: November 20
by Dave Clements 19 Nov '13

19 Nov '13

Hello all, The next GalaxyAdmins meetup will be Wednesday, November 20, at 10am US Central time. See the meetup page<http://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_11_20> for a link and directions for connecting to the meetup. *GCC2013 GalaxyAdmins BoF Followup* This is our first meetup since the GCC2013 GalaxyAdmins BoF<http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins> where we discussed what the group should focus on going forward, and what the Galaxy Project can do to support the group. As suggested at GCC2013, followup to that discussion will be the main topic for this meetup. We came out with several action items and one piece of unfinished business (leadership). Also, as suggested at the GCC2013 BoF, we would like to encourage discussion in the week before the meetup. Therefore, 1. Please review the notes from the GCC2013 GalaxyAdmins BoF<http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins> 2. Take a look at these two draft implementations of action items from that discussion: 1. Galaxy Deployment Pages<http://wiki.galaxyproject.org/Community/Deployments> 2. Galaxy Log Pages <http://wiki.galaxyproject.org/Community/Logs> And, if you see anything that you want to comment on please reply to this thread on the Galaxy-Dev list. I'll update other actions as the call gets closer. *Galaxy Project Update: Main moves to TACC* Nate Coraor will give the project update, focusing on the recent move of UseGalaxy.org to TACC. We hope to see (well, hear) you there, and please don't hesitate to ask if you have any questions. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Empty tool panel
by Yec'han Laizet 19 Nov '13

19 Nov '13

Hi, In the current version of galaxy stable branch (5c789ab4144a), the tool panel is empty when installed (freshly and out of the box) on my production server (ubuntu server 12.04). If I copy this galaxy folder onto my laptop, the tool panel shows up (ubuntu 13.10). Do you have an idea of what could be the problem? Thanks Yec'han ================================================ Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _________________________________ Plateforme Genome Transcriptome INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ================================================

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secure Galaxy with SSL
by Jingchao Zhang 19 Nov '13

19 Nov '13

Dear all, Today I installed the SSL module for our local Galaxy instance and the "https://" link is working fine. I added this "<Location "/"> RequestHeader set X-URL-SCHEME https </Location>" in our Apache configuration file as instructed in this webpage: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy Here are my problems with SSL: 1. Some build in links like "UCSC Main<http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl…> table browser" and "UCSC Test<http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-g…> table browser" become invalid. If I click on them, nothing will happen, as if they are blocked. 2. The old "http" link still works, which I think shouldn't because I added the "RequestHeader ... https" line in Apache configuration. I really want to disable the http link because the new users could be easily led to the old one. Both httpd and Galaxy have been restarted after the changes are made. Since I didn't find any similar threads in the mailist, I hope someone here can help me out with this. Thanks, Jim

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