- galaxy-dev - lists.galaxyproject.org

Can't change working directory during tool dependency installation
by Bruno Grande 25 Oct '14

25 Oct '14

I originally posted this question <https://biostar.usegalaxy.org/p/9401/> on the Galaxy Biostars, but later realized that galaxy-dev is probably more appropriate. So, here it goes. I'm trying to automate the installation of a tool's dependency with a tool dependency definition repository. During the package installation process, after moving the contents of a downloaded archive to the installation directory (*i.e.* $INSTALL_DIR), I simply want to change to that target directory away from the initial temporary working directory. However, I can't seem to change directory, either with a change_directory action or a cd shell_command action. Running pwd before and after attempting to change directory confirms this (see attached for installation log). I even made sure that $INSTALL_DIR is different from my initial working directory. Best regards, Bruno

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Citations tag not working
by James Mullan 24 Oct '14

24 Oct '14

Hello, I downloaded Galaxy a few months ago but I just noticed that the citations tag doesn't work on my download. The info on the hg pull I have is: hg tip changeset: 13771:7a4d321c0e38 branch: stable tag: tip user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Jul 30 11:13:20 2014 -0400 summary: Updated tag latest_2014.06.02 for changeset 8c30e91bc9ae What would I need to do if I wanted to include this functionality ? Regards jamesp J ames Mullan

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SLURM timeouts
by Sytchev, Ilya 24 Oct '14

24 Oct '14

Hi, I'm running a fork of galaxy-central latest_2014.08.11. The instance is configured to run jobs on a SLURM cluster. The problem is that the SLURM controller sometimes becomes too busy which results in errors like: galaxy.jobs.runners.drmaa INFO 2014-10-23 21:10:47,768 (1813/22896754) job left DRM queue with following message: code 1: slurm_load_jobs error: Socket timed out on send/recv operation,job_id: 22896754 This causes Galaxy to assume that the job has failed: galaxy.jobs.runners ERROR 2014-10-23 21:10:47,881 (1813/22896754) Job output not returned from cluster: [Errno 2] No such file or directory: '/n/regal/stemcellcommons/galaxy-stage/job_working_directory/001/1813/galax y_1813.o' This happens with both galaxy.jobs.runners.drmaa:DRMAAJobRunner and galaxy.jobs.runners.slurm:SlurmJobRunner. Is there any way to handle this condition in Galaxy? Thanks, Ilya

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filtering a <param> of type 'data' so only one type is available
by Dan Tenenbaum 24 Oct '14

24 Oct '14

Hi, I have a tool wrapper with a <param> of type="data". Currently, this renders as a text box with a drop down list that has 52 items in it (the number of things I have in my history, I guess). I'd like to filter this list so that only some items in the history (in my case any item whose name ends with '.rda') are shown in this dropdown. It seems like maybe the 'format' parameter to the 'param' tag is what I want, but: 1) I tried format="rda" and that didn't seem to change anything. 2) "rda" is not in the datatypes.conf file which the documentation suggests is required? (.rda is an extension used for serialized R objects.) The tool I'm working on only accepts rda files as input and the reason I'm asking for this is that it is all too easy to accidentally feed it a file of some other type. If the dropdown could be filtered so that only items which will work with the tool are shown, that would be great. Is there a way to do that? Thanks, Dan

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Determining galaxy api path automatically from a tool via dynamic_options?
by Dooley, Damion 23 Oct '14

23 Oct '14

After uploading my beta status tool to our test toolshed, I tried installing it on another of our galaxy servers but it wasn't able to find the api endpoint url. Is there a way to automatically do this within tool forms? I was hoping to avoid hardcoding this as part of the tool installation process. I'd thought I had it automated: In tool's form, a dynamic_options param <param name="api_url" display="radio" type="drill_down" label="For user with Galaxy API Key" dynamic_options="vdb_init_tool_user(__trans__)" /> was able to pass "trans" galaxy structure so I got as far as this python: self.api_url = 'http://' + trans.request.host ... but this yeilds http://acme.com/ rather than what's needed, the path to a particular installation: http://acme.com/galaxy/ I couldn't find a way to read the /galaxylab/ setting from the (slightly dated) universe_wsgi.ini config file - without say reading the file and parsing it. Is there an __app__.config.prefix or somesuch variable where this info is? Thanks! Damion

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2bit to FASTA tool
by Freese, Nowlan 23 Oct '14

23 Oct '14

To Whom it May Concern, Would it be possible to add a way to convert 2bit files to FASTA within Galaxy? We would like IGB users to be able to pull genome files (in 2bit) directly from the IGBQuickload site into Galaxy, convert them to FASTA and then use that to align against. This way a user could start with the IGBQuickload site, move to Galaxy for analysis, and then view the data in IGB without ever having to use the command line. Thank you! Nowlan Freese Postdoctoral Research Fellow UNC Charlotte IGB Team

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hg38
by Mark Lindsay 22 Oct '14

22 Oct '14

Dear All have very little experience in this area and probably making a very basic mistake but I am trying to load the hg38 reference genome into a local instance of galaxy (not installed by myself) using ‘Create DBkey and reference genome’ using ‘hg38’ in the UCSC DBkey option box(es) but keep getting the following error message either ‘invalid DBkey” or 'Exception: Unable to determine filename for UCSC Genome for hg38: ['.', '..', 'est.fa.gz', 'est.fa.gz.md5', 'mrna.fa.gz', 'mrna.fa.gz.md5', 'refMrna.fa.gz', 'refMrna.fa.gz.md5', 'xenoMrna.fa.gz', 'xenoMrna.fa.gz.md5', 'xenoRefMrna.fa.gz', 'xenoRefMrna.fa.gz.md5', 'analysisSet', 'README.txt', 'hg38.2bit', 'hg38.agp.gz', 'hg38.chromFa.tar.gz', 'hg38.chromFaMasked.tar.gz', 'hg38.fa.align.gz', 'hg38.fa.gz', 'hg38.fa.masked.gz', 'hg38.fa.out.gz', 'hg38.trf.bed.gz', 'md5sum.txt’] Could anybody point me in the right direction? Many Thanks Mark

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Uploading workflow to toolshed
by Mikel Egaña Aranguren 22 Oct '14

22 Oct '14

Hi; We are developing a Metagenomics tool suite (along the lines of Mothur) and we would like to include some example workflows. What is the best practice to upload workflows to the tool shed? - As part of the tool suite. - In a separate repository with only the workflows. Thanks -- Mikel Egaña Aranguren, Ph.D. http://mikeleganaaranguren.com

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Re: [galaxy-dev] Blast+ Wrapper: blastdbcmd: range parameter
by Peter Cock 22 Oct '14

22 Oct '14

Thanks, https://github.com/biopython/biopython/pull/385 You can't (yet) do this via the BLAST wrappers. You would have to pull out the full sequences using the makeblastdb wrapper, then edit them with another Galaxy tool. Or work directly from the FASTA file if you have it. Peter On Wed, Oct 22, 2014 at 6:57 AM, Matthias Enders <m.enders(a)german-seed-alliance.de> wrote: > Hi Peter, > > I added a new Issue, hope everything is correct. > > Kind regards, > Matthias Enders > > > -----Ursprüngliche Nachricht----- > Von: Peter Cock [mailto:p.j.a.cock@googlemail.com] > Gesendet: Tuesday, October 21, 2014 11:25 PM > An: Matthias Enders > Cc: galaxy-dev(a)lists.bx.psu.edu > Betreff: Re: [galaxy-dev] Blast+ Wrapper: blastdbcmd: range parameter > > Hi Matthias, > > Can you file an issue here about adding this here please? > https://github.com/peterjc/galaxy_blast > > Thanks! > > Peter > > On Tue, Oct 21, 2014 at 10:36 AM, Matthias Enders <m.enders(a)german-seed-alliance.de> wrote: >> Hello all, >> >> I use the ToolShed NCBI Blast+ Wrappers (https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c) and I tried to retrieve sequence information from databases. >> >> The blastdbcmd comes with the feature to extract a given range of the sequence: >> >> -Range string Range of sequence to extract (Format: start-stop) >> >> Is this parameter / functionality also part of the wrapper, how can I use this functionality? >> >> Thanks, >> Matthias >> >> >> ___________________________________________________________ >> 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/

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Blast+ Wrapper: blastdbcmd: range parameter
by Matthias Enders 21 Oct '14

21 Oct '14

Hello all, I use the ToolShed NCBI Blast+ Wrappers (https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c) and I tried to retrieve sequence information from databases. The blastdbcmd comes with the feature to extract a given range of the sequence: -Range string Range of sequence to extract (Format: start-stop) Is this parameter / functionality also part of the wrapper, how can I use this functionality? Thanks, Matthias

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