- galaxy-dev - lists.galaxyproject.org

igv integration
by Langhorst, Brad 05 Feb '14

05 Feb '14

I’m having some trouble with igv integration… it works fine for hg19, but for other this influenza genome i just added, i’m seeing from IGV [cid:9C974C45-560B-46C3-AF75-CC794D0D1ACD@neb.com] Any idea what I’m doing wrong? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist

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Cluster nodes without NFS access to galaxy-dev.
by Luca Toldo 05 Feb '14

05 Feb '14

dear All, my galaxy server can NFS share its disks with the head of the cluster, however the compute nodes cannot see those disks since they can see only what the head of the cluster provides. My cluster nodes are diskless. I'd appreciate advice, if someone had already installed galaxy in such configuration. Unfortunately installing galaxy-dev on the head of the cluster is not an option. Looking forward your advice. Luca

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Running tools from within a tool
by Ketan Maheshwari 05 Feb '14

05 Feb '14

Hi, This is a question I posted to galaxy user mailing list a while back and was redirected to dev for possible answers: Is it possible in Galaxy to design a tool whose sole purpose is to run other tools. This is motivated by our desire to enhance execution capabilities of existing tools via a generic tool which acts as a wrapper. Thanks, Ketan

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Upload via FTP - Assertion Error on Change ownership of working dictory
by Adam Brenner 05 Feb '14

05 Feb '14

Howdy, I am having trouble uploading data on our local instance of Galaxy here. The method is via FTP and here is the error I am seeing in the logs: galaxy.jobs.runners DEBUG 2014-01-30 14:29:31,987 execution of external set_meta for job 1367 finished galaxy.jobs DEBUG 2014-01-30 14:29:32,016 (1367) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /som/galaxy/database/job_working_directory/001/1367 root 0 galaxy.jobs ERROR 2014-01-30 14:29:32,058 (1367) Failed to change ownership of /som/galaxy/database/job_working_directory/001/1367, failing Traceback (most recent call last): File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line 870, in finish self.reclaim_ownership() File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line 1316, in reclaim_ownership self._change_ownership( self.galaxy_system_pwent[0], str( self.galaxy_system_pwent[3] ) ) File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line 1302, in _change_ownership assert p.returncode == 0 AssertionError Any idea on how to fix the issue? Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences System Administrator, HPC Cluster Office of Information Technology http://hpc.oit.uci.edu/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

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tools fails only in workflow
by Christian Hundsrucker 05 Feb '14

05 Feb '14

Dear all, I developed a tool which allows an optional selection as input amongst others. It works quite neat if I run it via "Analyse Data". Actually, it only breaks in one condition: If I try to run it "as a Workflow" and set the "multiple selection input" to be set at runtime AND do not select anything at runtime it'll raise a Cheetah error. Even if I select nothing but prior to runtime as workflow it works fine again. The multiple selection is based on a data table/ loc-file. Any ideas? Cheers, Christan relevant tool specification snippet: --------------------------------------------- [...] <param [...] type="select" optional="true" multiple="true" display="checkboxes" [...]> <options from_data_table="fmi_[...]"/> </param> [...] Cheetah error: -------------------- Traceback (most recent call last): File "[...]/galaxy/galaxy_dist/lib/galaxy/jobs/runners/__init__.py", line 123, in prepare_job job_wrapper.prepare() File "[...]/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 702, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "[...]/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2639, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "[...]/galaxy/galaxy_dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "[...]/galaxy/galaxy_dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1391423600_85_54475.py", line 89, in respond File "cheetah_DynamicallyCompiledCheetahTemplate_1391423600_85_54475.py", line 89, in <lambda> IndexError: list index out of range Galaxy: ---------- changeset: 11219:5c789ab4144a branch: stable

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Cheetah code issue
by Ketan Maheshwari 04 Feb '14

04 Feb '14

Hi, While developing a tool, I am facing Cheetah code issue. I looked up the mailing list archive and found many similar issues reported earlier but could not debug this. Any tips in debugging is appreciated. File "cheetah_DynamicallyCompiledCheetahTemplate_1391530084_29_71368.py", line 97, in respond NotFound: cannot find 'rngstart' Attached is the xml tool definition file. Best, Ketan

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How to install tool-shed behind proxy with authentication ?
by Luca Toldo 04 Feb '14

04 Feb '14

dear Galaxians, my server is behind a proxy with user authentication. Wget and hg work fine however unfortunately when I try to install from the tool shed I get error since the system is using urllib2 that is known not to be compatible with proxy with authentication. How should one locally install tool-sheds ? Is it possible with hg or with wget ? Looking forward your advice. Thankyou

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Indexes separator in tool
by Bossers, Alex 03 Feb '14

03 Feb '14

Not sure if this question or solution has passed this list already but couldn't find anything in the archive. Is it possible to somehow insert separator lines between groups of for instance bowtie2 indexes? One of our tool displays it like below (the ----- lines); I would like to add separators but as below is ugly but working. Tried to make them boldface but doesn't work. I now linked an almost empty index. At best the checkmark should not show up also. Could this be done somehow from the bowtie2.loc file? This becomes extreme handy when you have a large collection of indexes. Alex This code in the tool xml loads the index; <param name="bowtieindexes2" type="select" label="Select genome sets for alignment" help="" display="checkboxes" multiple="True" > <options from_data_table="bowtie2_indexes"> <column name="name" index="2"/> <column name="value" index="3"/> <validator type="no_options" message="No indexes are available" /> </options> </param> And shows up in the tool like; Example: ----------------- Mammals ----------------- Bos taurus ensembl 4.0.61 Homo sapiens ensembl GRch37 Macaca mulatta (rhesus monkey draft NCBI) Etc etc ----------------- Other Eukaryotes ----------------- Musquito aedes_aegypti draft Saccaromyces cerevisiae Etc etc etc etc ----------------- Prokaryotes ----------------- E coli refseq U00096 Etc etc etc Waddlia chondrophila strain 2032/99 draft jan2014 Waddlia chondrophila WSU86-1044 chrom Waddlia chondrophila WSU86-1044 plasmid ----------------- Contaminants ----------------- Common NGS adpaters UniVec vector DB PhiX (internal NGS control)

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local galaxy instance can't recognize file format!!
by JU HUCK LEE 01 Feb '14

01 Feb '14

Dear Galaxy team, I have recently made local galaxy instance in my computer (since my labtop is window, I used virtualbox to install linux) to use some workflow made by other people (for finding bacterial non-coding RNA, the name of workflow is DETR'PROK). After I finally installed the local galaxy instance in my labtop(it was not easy because I haven't used linux system before), I uploaded my RNA-seq mapping data(bam file),which I did in galaxy main, through genomespace. However, my local galaxy instance can't recognize file format; it looks like that it can only recognize file format when I uploaded the files from my computer (when I use galaxy main, it is no problem to upload files from genomespace). So, I uploaded gff, fasta and bam files, but I got a error for my bam file. Please let me know what was wrong. I really want to use above workflow to find bacterial non-coding RNA which I can't do in galaxy main. Thank you, Ju Huck Lee ps. since I got this "Mail is not configured for this galaxy instance" when I clicked the report, I attached the screen with my error; please let me know how I can report my errors through my local galaxy instance. one more question; why the manage data in Admin is beta, so I couldn't use it.

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Re: [galaxy-dev] Remote User Logout
by Tim Booth 01 Feb '14

01 Feb '14

Hi, I'm currently using one of those hacks, and it seems to work nicely for the user (Chrome + FF at least) but it does need some messy setting up in Apache and some cunning redirects in place. I've pasted the relevant file fragments below. It's somewhat confounded with my stuff to enable SFTP uploads but hopefully you get the idea and the original explanation on Stackoverflow is pretty good. The remote_user_logout_href is something I got to by trial and error. Cheers, TIM === % cat /usr/share/galaxy-server/logout/.htaccess # HaCk based on http://stackoverflow.com/questions/4163122/http-basic-authentication-log-out # Authname must match the one in ../proxy/.htaccess AuthType Basic AuthName Galaxy_Server AuthUserFile /usr/share/galaxy-server/logout/.htpasswd Require user logout === % cat /usr/share/galaxy-server/logout/.htpasswd #Password is logout. This in not a secret. logout:$apr1$0eB1iURY$kwqa0c8tXksbjPQLYqr6s. === % cat /usr/share/galaxy-server/proxy/.htaccess # Security settings for Galaxy proxied via Apache. Note the actual # proxy config is under /etc/apache2/conf.d/galaxy. If for some # reason you wanted Apache proxy with internal Galaxy authentication # then you could remove this file and Apache would no longer insist on # authentication. AuthBasicProvider external AuthExternal pwauth AuthType Basic AuthName Galaxy_Server #I'd like to do this, but it upsets Firefox. Use ErrorDocument instead. # AuthName "Galaxy Server: \ # Log in with regular username and password. \ # Users need to be in the galaxy system group." ErrorDocument 401 "<html>\ <title>401 Authorization Required</title>\ <h1>Log-in to Galaxy failed</h1>\ <p>You should have been prompted to log into the Galaxy server. \ You need to give your regular system username and password. \ Please reload this page to try again.</p>\ <p>If this fails, check that you are a member of the galaxy system group, by \ running <code>groups</code> on the command line.</p>\ <p>To add a user, eg. user1, to this group, you may use the command:</p>\ <ul><li><code>sudo usermod -aG galaxy user1</code></ul></li>\ </html>" # You may want to comment these 2 lines out or to # change the group required, but users still need to # be in the galaxy group for SFTP uploads to work properly. AuthzUnixgroup on Require group galaxy # This is needed to tell Galaxy about the remote # user. RequestHeader set REMOTE_USER %{RU}e env=RU RequestHeader unset Authorization env=RU === % cat /etc/galaxy-server/universe_wsgi.d/31_apache-proxy.ini # Settings added by debian-galaxy-apache-proxy to switch Galaxy over to # authenticating by real user accounts and also permitting uploads. [app:main] # Other scripts assume that maildomain is localhsot, so you can't just # change the setting below and expect everythig to work. use_remote_user = True remote_user_maildomain = localhost # Users may copy files here directly or upload via SFTP/SCP ftp_upload_dir = /var/lib/galaxy-server/transfer ftp_upload_site = *** Transfer files via SCP or SFTP to /var/lib/galaxy-server/transfer/... *** # There is no neat way to log out a user with Basic Auth, but here is a non-neat way. # Not yet tested on IE. remote_user_logout_href = javascript:var r=new XMLHttpRequest();r.onreadystatechange=function(){if(r.readyState==4)window.location.replace('logout.html')};r.open('get','logout.html',true,'logout','logout');r.send(); === -- Tim Booth <tbooth(a)ceh.ac.uk> NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705

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