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Workflow editor stuck on loading workflow
by Ryan G 27 Jul '15

27 Jul '15

It looks like a recent commit since 6/26 to 15.05 is break the workflow editor. I have a pipeline I'm trying to edit. I updated my instance of Galaxy and now when I try to edit a workflow, the editor is stuck at "Loading workflow editor".

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Switching history doesn't work with prefix
by Ping Luo 24 Jul '15

24 Jul '15

Hello, Our galaxy server is served under a sub-directory "/myserver". So far everything works except the "Switch to" button in "view all history". When clicking it, there is no response. From apache server access log, I see this message "GET /history/set_as_current?id=9a8f74b3b768f8f1 HTTP/1.1" 404 304 And in the apache error log, I see File does not exist: /www/htdocs/history, referer: https://xxx.xxx.xxx/myserver/history/view_multiple Since the prefix "/myserver" is not properly prepended in the equest, the request is not properly routed. It tries to retrive the history page from the document root /www/htdocs. So far, all other requests seems have a proper prefix, for example "GET /myserver/history/current_history_json HTTP/1.1" 200 1430 "GET /myserver/api/histories/7a11fc800eeb71e9/contents HTTP/1.1" 200 15876 "GET /myserver/history/view_multiple HTTP/1.1" 200 27296 "GET /myserver/static/style/base.css?v=1437576796 HTTP/1.1" 304 - Please help to resolve the issue. Thanks, Ping

3 6

Tool Versions not displaying in a predictable way in the tool menu
by Lance Parsons 22 Jul '15

22 Jul '15

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"Failure when preparing job" on blastp
by Peter van Heusden 22 Jul '15

22 Jul '15

Hi there I'm trying to use the blastp tools from the ncbi_blast_tools, but every time I try and run a job I get the following error: Traceback (most recent call last): File "/net/ datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py", line 163, in prepare_job job_wrapper.prepare() File "/net/ datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py", line 859, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/net/ datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py", line 422, in build raise e NotFound: cannot find 'files_path' while searching for 'db_opts.histdb.files_path' This is happening when expanding the tool template. The BLAST db in in the history (thus the reference to histdb) but why can it not find this attribute? Peter

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Object-Store, setting filetypes crashes Galaxy
by bjoern.gruening＠googlemail.com 22 Jul '15

22 Jul '15

Hi, I have configured to use the hierarchical object store but as soon as I try to reset the filetpye of a dataset Galaxy is crashing with: galaxy.objectstore DEBUG 2014-06-12 14:39:21,180 Using preferred backend 'files3' for creation of MetadataFile 5963 132.230.153.57 - - [12/Jun/2014:14:39:20 +0200] "POST /datasets/966f24627ef70c12/edit HTTP/1.1" 500 - " http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit" "Mozilla/5.0 (X11; Linux x86_64; rv:29.0) Gecko/20100101 Fire fox/29.0" Error - <type 'exceptions.OSError'>: [Errno 2] No such file or directory: 'database/tmp/metadata_temp_file_1xnGcE' URL: http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 295 in edit trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':data }, overwrite = False ) #overwrite is False as per existi ng behavior File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py', line 18 in execute overwrite, history, job_params ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py', line 79 in execute_via_app kwds = { 'overwrite' : overwrite } ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line 717 in setup_external_metadata shutil.copy( dataset.metadata.get( meta_key, None ).file_name, metadata_temp.file_name ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line 575 in file_name self._filename = abspath( tempfile.NamedTemporaryFile( dir = self.tmp_dir, prefix = "metadata_temp_file_" ).name ) File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 454 in NamedTemporaryFile (fd, name) = _mkstemp_inner(dir, prefix, suffix, flags) File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 235 in _mkstemp_inner fd = _os.open(file, flags, 0600) OSError: [Errno 2] No such file or directory: 'database/tmp/metadata_temp_file_1xnGcE' I have attached my object_store_conf.xml file. Thanks, Bjoern

5 7

Connection reset by peer
by COUNTOURIS Hector 21 Jul '15

21 Jul '15

Hello, i'm actually having a message of "connection reset by peer" when i'm launching a long API request (upload files only links actually, run the workflow other them and retrieve the results into a specific folder). The workflow is working fine when i proceed to an analysis file by file but when it comes to several file processing (like 10 or more), this exception appear. I'm working with Bioblend on a local instance with a postgres SGBD. I've perfom the database performance enhancement you suggest for production mode. But right know i don't have any Apache or Nginx server. Is that mandatory ? Thanks in advance for your help. Best regards. HC.

2 1

Fwd: Re: Change from Bitbucket to git
by Jochen Bick 21 Jul '15

21 Jul '15

Hej Jelle, I also thought of setting it up again from scratch... @Marius I will check again the hg diff. The update with hg update worked fine as far as I can see. So I'm not in a big hurry to change to git. Cheers Jochen On 21.07.2015 13:27, Jelle Scholtalbers wrote: > Hi Jochen, > > I recently took a probably more labour intensive approach. > > # backup! > # mv prev-installation to somewhere else > # git clone to old-location > # git checkout -b master origin/master > # and copy over every config, tool xml, tool dependency directory, > tool-data loc files from the prev-installation to the new git one > # add your own code changes if you have any that you want to keep > # ./run.sh or manage_db.sh upgrade > # check log and probably copy some more missing files > > The upside for me was that I could finally remove all the junk that our > installation has been collecting for the last couple of year. > > Cheers, > Jelle > > > On Tue, Jul 21, 2015 at 12:45 PM, Jochen Bick <jochen.bick(a)usys.ethz.ch> > wrote: > >> Thanks Marius, >> >> it does not look like it's working for me. There are to many changes in >> git diff... >> >> the git pull and cat local_changes.diff |patch -p1 -R gives me an >> endless list of differences. >> >> Cheers Jochen >> >> On 21.07.2015 11:41, Marius van den Beek wrote: >>> Hi Jochen, >>> >>> I recently did this. Instructions are here: >>> https://wiki.galaxyproject.org/Develop/SourceCode >>> >>> This has worked for me: >>> (~/galaxy-dist is my production galaxy dir) >>> cd ~ >>> git clone https://github.com/galaxyproject/galaxy.git >>> cd galaxy >>> git reset --hard 3f1cec451f6dadee52a70a14fc6f6899f7aacdae >>> cd ~/galaxy-dist >>> hg update 17115 >>> mv .hg .hg_backup >>> cp -R ~/galaxy/.git . >>> git pull (at this point I got a merge error!) >>> so I did: >>> git diff > local_changes.diff >>> cat local_changes.diff |patch -p1 -R >>> git pull >>> git checkout release_15.05 >>> >>> Best, >>> Marius >>> >>> On 21 July 2015 at 11:36, Jochen Bick <jochen.bick(a)usys.ethz.ch> wrote: >>> >>>> Hi, >>>> >>>> is it possible to change from bitbucket to git? So I would like >>>> future-update my galaxy from git instead from bitbucket. >>>> >>>> Cheers Jochen >> ___________________________________________________________ >> 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/ >> > -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 Office: Tannenstrasse 1 / TAN D 6.2 8092 Zurich, Switzerland Phone +41 44 632 28 25 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

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Change from Bitbucket to git
by Jochen Bick 21 Jul '15

21 Jul '15

Hi, is it possible to change from bitbucket to git? So I would like future-update my galaxy from git instead from bitbucket. Cheers Jochen

3 3

Possible bug on "Create a collection of paired datasets"
by Ata Roudgar 21 Jul '15

21 Jul '15

Hi, I am a computer cluster admin and I am trying to install galaxy on our cluster. I used galaxy-release_15.05 and because we need to serve Galaxy at a sub directory, e.g. irida-galaxy I modified the options prefix and cookie_path in the galaxy configuration file as follow: prefix = /irida-galaxy filter-with = proxy-prefix cookie_path = /irida-galaxy We use apache as an interface with the Following configuration: <Proxy http://localhost:9010> Order deny,allow Allow from all </Proxy> RewriteRule ^/irida-galaxy$ /irida-galaxy/ [R] RewriteRule ^/irida-galaxy/static/style/(.*) /home/irida/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/irida-galaxy/static/scripts/(.*) /home/irida/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/irida-galaxy/static/(.*) /home/irida/galaxy-dist/static/$1 [L] #RewriteRule ^/irida-galaxy/favicon.ico /home/irida/galaxy-dist/static/favicon.ico [L] RewriteRule ^/irida-galaxy/robots.txt /home/irida/galaxy-dist/static/robots.txt [L] RewriteRule ^/irida-galaxy(.*) http://localhost:9010$1 [P] Everything works fairly good. Now I want to create a Dataset Pairs. first I uploads some fastaq files, e.g., a_1.fastaq a_2.fastaq b_1.fastaq b_2.fastaq c_1.fastaq c_2.fastaq then I choose: "Build List of Dataset Pairs" (See Fig-1 attached) There is a window appears on my screen with the title: Create a collection of paired datasets. Now I am able to choose a name and save the paired collection. However, once I click on "Create list" buttons I receive a error message on top of the windows: "An error occurred While creating this collection: Not found See Fig-2 attached. To be able to search the cause of error I turn on the "Browser Consul" on my web browser and notice that the error is related to the following web form post: https://newrobson.westgrid.ca:8444/api/histories/4936629215c25989/contents/… Which makes sense because such address do not exist. The address should be https://newrobson.westgrid.ca:8444/irida-galaxy/api/histories/4936629215c25… So the prefix (irida-galaxy) is missing before /api/histories...../dataset_collection Is it a bug or am I missing something? Please note that such error does not appear when I do not use prefix in my galaxy configration. Thanks for your time, Cheers, Ata ---- Ata Roudgar Research Computing WestGrid Site IT Services Simon Fraser University Burnaby, British Columbia Canada V5A 1S6 phone: 778 782-8860 fax: 778 782-4242

2 2

Troubleshooting
by Lionel Mavoungou 21 Jul '15

21 Jul '15

Hello, I have a problem when I try to align en FATSQ file for a ChIP-seq. I have done a FASTQ grooming because it has been performed on Illumina. No my file is a .FASTSANGER. However my file is not recognized. I see this : No fastqsanger, fastqillumina or fastqsolexa dataset collection available. How could I fix it. It seems that my fastq file as well as my fastqsanger are not recognized. Thanks a lot, Lionel

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