October 2016 - galaxy-dev - lists.galaxyproject.org

Error on chemfp version 1.1p1 installation
by Léo Biscassi 26 Oct '16

26 Oct '16

Hi all, I'm trying install chemical toolbox on a local instance and I got an error the following error raised by chemfp dependency: File "/home/leobiscassi/programs/galaxy-local/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/home/leobiscassi/programs/galaxy-local/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 181, in url_download raise Exception( err_msg ) Error downloading from URL http://chem-fingerprints.googlecode.com/files/chemfp-1.1p1.tar.gz: HTTP Error 404: Not Found This link is the same it's in cargo-port [1], but isn't working, can you help me? [1] https://github.com/galaxyproject/cargo-port/blob/master/urls.tsv#L396 -- Best regards, *Léo Biscassi*

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Fwd: Workflow Execution Files
by Katherine Beaulieu 25 Oct '16

25 Oct '16

---------- Forwarded message ---------- From: Katherine Beaulieu <katherine.beaulieu014(a)gmail.com> Date: Mon, Oct 24, 2016 at 2:55 PM Subject: Re: [galaxy-dev] Workflow Execution Files To: Aysam Guerler <aysam.guerler(a)gmail.com> Awesome thanks Aysam! I was wondering if you know what happens to the job parameters once they go through 'POST'? I am trying to add my own parameter which should show up in the database. I was successful for an individual job in tool-form.js, by just adding an attribute to the job_def.inputs parameter but in tool-form-composite.js, just adding a parameter to job_def.parameters[step size][job_input_id] doesn't automatically add to the database. Thanks for the help! On Mon, Oct 24, 2016 at 9:57 AM, Aysam Guerler <aysam.guerler(a)gmail.com> wrote: > Hi Katherine, > > The tool form is build and submitted to the API through > tool-form-composite.js. > > Sam > > On Mon, Oct 24, 2016 at 9:29 AM, Katherine Beaulieu < > katherine.beaulieu014(a)gmail.com> wrote: > >> Hi Everyone, >> Does anyone know what files workflow execution goes through? I had >> assumed it just went through the same files as individual jobs for each >> step but I don't think that's the case. I was looking at tool-form.js but >> it doesn't seem to be executing that file. >> Thanks! >> Katherine >> >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > >

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Galaxy Pulsar unable to access DRMAA so
by Yip, Miu ki 24 Oct '16

24 Oct '16

Hi all, When trying to submit a job to the cluster via Pulsar from Galaxy, an error is thrown and the job won’t be submitted. The paster.log file has the following error: Exception: Attempt to use DRMAA, but DRMAA Python library cannot be loaded. OSError - problem loading shared library [/opt/uge/lib/lx-amd64/libdrmaa.so: cannot open shared object file: No such file or directory]. The shared object file can be found and accessed manually. Am not sure what this error means or how to go about looking for more information. Thank you in advance for your help. Best, Miuki

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upload data error
by Beginner TI 24 Oct '16

24 Oct '16

Hi, I'm trying to upload a file to a new galaxy instance for the first time, however an error happened, which never did in the past: Traceback (most recent call last): File "/media/libraryfiles/galaxy/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job job_wrapper.prepare() File "/media/libraryfiles/galaxy/lib/galaxy/jobs/__init__.py", line 893, in prepare tool_evaluator.set_compute_environment( compute_environment, get_special=get_special ) File "/media/libraryfiles/galaxy/lib/galaxy/tools/evaluation.py", line 63, in set_compute_environment visit_input_values( self.tool.inputs, incoming, validate_inputs ) File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 92, in visit_input_values visit_input_values( input.inputs, d, callback, new_name_prefix, new_label_prefix, parent_prefix=new_name_prefix, **payload ) File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 110, in visit_input_values callback_helper( input, input_values, name_prefix, label_prefix, parent_prefix=parent_prefix, context=context ) File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 75, in callback_helper new_value = callback( **args ) File "/media/libraryfiles/galaxy/lib/galaxy/tools/evaluation.py", line 62, in validate_inputs input.validate( value, request_context ) File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/basic.py", line 198, in validate validator.validate( value, trans ) File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/validation.py", line 99, in validate raise ValueError( message ) ValueError: You will need to reselect the file you specified (/media/8tb/galaxy-data-store/database/tmp/upload_file_data_5wWKi5). It looks those files were successfuly uploaded, but the dataset files are all empty. Has anyone seen this? Thanks, Rui

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Workflow Execution Files
by Katherine Beaulieu 24 Oct '16

24 Oct '16

Hi Everyone, Does anyone know what files workflow execution goes through? I had assumed it just went through the same files as individual jobs for each step but I don't think that's the case. I was looking at tool-form.js but it doesn't seem to be executing that file. Thanks! Katherine

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Tool needs a particular file extension
by Steve Cassidy 24 Oct '16

24 Oct '16

Hi, I’m wrapping a tool that needs it’s input to have a known file extension (an audio file, eg. .wav). Since Galaxy stores all data as .dat files the tool is falling over since it doesn’t know what .dat is. I thought I’d be able to get around this by hard linking the .dat file to the same name with a .wav extension (dataset_1.dat.wav), this works when I try it with the tool on the command line but within Galaxy it fails, here’s my <command>: ln $signal ${signal}.wav & /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$language BPF=$bpf INSKANTEXTGRID=$inskantextgrid INSORTTEXTGRID=$insorttextgrid MODUS=$modus MAUSSHIFT=$mausshift MINPAUSLEN=$minpauslen WEIGHT=$weight INSPROB=$insprob NOINITIALFINALSILENCE=$noinitialfinalsilence OUTSYMBOL=$outsymbol OUT=$output SIGNAL=${signal}.wav resulting in the job command line: ln /tmp/tmp7AZvx7/files/000/dataset_2.dat /tmp/tmp7AZvx7/files/000/dataset_2.dat.wav & /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=aus BPF=/tmp/tmp7AZvx7/files/000/dataset_1.dat INSKANTEXTGRID=false INSORTTEXTGRID=false MODUS=standard MAUSSHIFT=10 MINPAUSLEN=5 WEIGHT=7.0 INSPROB=0.0 NOINITIALFINALSILENCE=no OUTSYMBOL=sampa OUT=/tmp/tmp7AZvx7/files/000/dataset_3.dat SIGNAL=/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav I’m getting an error message from the tool: sox FAIL formats: can't open input file `/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav': WAVE: RIFF header not found this suggests that the hard link didn’t get made. I tried copying the file instead but got the same result. I could go in and patch the tool script to be more forgiving but it would be good to find a solution that didn’t require that if possible. Any pointers appreciated. Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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question about galaxy supported datastore
by Beginner TI 23 Oct '16

23 Oct '16

Hi, A couple days ago, I was having problem with uploading data to Galaxy. I had no clue why this happened. Seems some kind of validator didn't pass. Here is the message: You will need to reselect the file you specified I searched and found this error message is in galaxy release before, but not in this release: <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator>  My understanding of this comment is that user needs to select a file as the input file. It could not be set due to security reasons. I didn't get it...still confused. However, today I found that we are using an external 8tb drive that is physically attached on another host as the data store. Seems postgresql takes it well, but galaxy doesn't. The file system is CIFS. When I looked at the permissions, there is a + at the end, but when I use getfacl, I don't see anything besides the regular user/group/other. In ths past we have used external drives directly connected to the galaxy instance and it always worked. So...does galaxy not support disks not physically attached?? I feel this is less likely, maybe what I'm seeing is a coincidence? What exactly caused this? Any input will be greatly appreciated. :-) Thanks, Rui

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Changing Tool Shed URL
by Youssef GHORBAL 21 Oct '16

21 Oct '16

Hello, I’m wondering if there is any way to change an established Tool Shed URL. I have a Galaxy instance and a Tool Shed instance (http://mytoolshed.url/xxx) A lot of tools have beed installed from that Tool Shed inside Galaxy (tools referenced inside workflows etc) I want to change the Tool Shed URL from http://mytoolshed.url/xxx to http://mytoolshed2.url/yyyy. Galaxy and Tool Shed seems to use parts of the URL as a guid for tools. Tool Shed does not seem to bother to be called by either URLs (it generates guids with the new URLs scheam for new tools though) Galaxy does not seem to handle it, I changed the tool_sheds_conf.xml to point to new URL, but when I update a tool on the Tool Shed, Galaxy gets the new version but it generates buggy tool panel (the tool is cited twice) I also tried to mess around with the shed_tool_conf.xml apdapting the guids and the <tool_shed> items with no luck. Can someone point me to the right direction ? How the matching is done between shed_tool_conf.xml entries, the tool_version and tool_shed_repository tables. Thank you for your help. Youssef Ghorbal Institut Pasteur

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Data Library Import "Click this to start analyzing it." requires relogin
by D K 20 Oct '16

20 Oct '16

Hi Galaxy-devs, On my local instance of Galaxy (v16.07) when a user imports a shared data library file into their history and clicks on the "Selected datasets imported into history. Click this to start analyzing it." popup, they get directed back to the Galaxy log in page regardless if they are already logged in. Does this have to do with my settings in galaxy.ini? This behavior does not occur on usegalaxy.org. Any suggestions would be appreciated. Thanks! DK

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Wrapper for the MISO programs
by evan clark 20 Oct '16

20 Oct '16

I am currently working to create a wrapper for the MISO tools and wanted to see if anyone has previously developed a functional or semi-functional wrapper for it.

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