- galaxy-dev - lists.galaxyproject.org

removing inputs from a pipeline
by Philipe Moncuquet 08 Apr '13

08 Apr '13

Hi Dev, Is there a way to automatically delete inputs in a pipeline ? Let say you don't want to keep your raw data because of quotas issues and you want your pipeline to do it rather than to do it manually. Regards, Philippe

2 1

setup grid engine
by Jingzhi Zhu 08 Apr '13

08 Apr '13

I have downloaded the 04_01 release and tried to configure the Sun Grid Engine so that the job can run on our cluster. I have export the DRMAA_LIBRARY_PATH environment variable (export DRMAA_LIBRARY_PATH=/home/love-galaxy/bin/libdrmaa.so.1.0). Then copy job_conf.xml.sample_advanced to job_conf.xml. I have deleted some lines on the plugins section so it looks like this in job_conf.xml <plugins workers="4">  <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAARunner"/> </plugins> The run.sh returns the following error galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,465 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,466 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2013-04-08 15:57:12,472 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2013-04-08 15:57:12,474 Starting job handler galaxy.jobs.runners DEBUG 2013-04-08 15:57:12,475 Starting 4 LocalRunner workers galaxy.jobs DEBUG 2013-04-08 15:57:12,477 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' Traceback (most recent call last): File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 37, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/app.py", line 159, in __init__ self.job_manager = manager.JobManager( self ) File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31, in __init__ self.job_handler = handler.JobHandler( app ) File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 29, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 543, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins() File "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 476, in get_job_runner_plugins runner_class = getattr( module, class_name ) AttributeError: 'module' object has no attribute 'DRMAARunner' Can someone point to me what is going on here? If you have configured the SGE successfully with the latest 4.1 release, can you show me what the file job_conf.xml should look like? There are a lot of tags in this new XML file and I found it is hard to do it right. Thanks! Jingzhi

2 1

Galaxy + ProFTPd - proper configuration / uploaded files not accessible in Galaxy
by Jan Hapala 08 Apr '13

08 Apr '13

Hi, I am new to Galaxy. I have managed to set up my Galaxy server with PostgreSQL and ProFTPd. I only do not know how to configure the system properly in order to get uploaded files into Galaxy. Problems: 1. I cannot see the files uploaded through ProFTPd from Galaxy. 2. I cannot upload any (even tiny) file through the Galaxy web interface -- Galaxy puts the upload task in the queue and the arrow is blinking (like it is uploading) but it never ends. Problem nr. 1 is solved when I set the current user's home directory access rights to 777. But it does not seem to be the best solution (and the ProFTPd config file shown in http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP is more restrictive than that). I run Galaxy under UNIX user called galaxyuser. And I log into Galaxy as someone(a)somewhere.com. The access rights on the folders are as follows: drwx--x--x 3 galaxyuser root 4096 dub 5 12:05 /var/ftp_uploads/ /var/ftp_uploads/: total 4 drwx------ 2 65533 65533 4096 dub 8 15:38 someone(a)somewhere.com I would appreciate any suggestions. Best regards, Jan

2 2

History periodically disappears in AWS Cloudman installation
by Greg Edwards 08 Apr '13

08 Apr '13

Hi, We're running a private Cloudman Galaxy on AWS for small-scale proteomics work. Lately the whole History of the main user id we use has occasionally disappeared, ie. on login the History is empty. The datasets aren't hiding in "Deleted Datasets". They appear to still be there in /mnt/galaxyData/files/000. They're not in the Anonymous (not logged in ) id. They're not in another id. The data doesn't come back later. We reload the latest datasets in use and the numbering in the history restarts from 1. We're running the most basic config, with the simple single-threaded database. Nothing of interest seems to be in the various Cloudman logs. I've searched the archives for "lost/deleted/disappeared datasets/history" etc but nothing useful turned up. This is our rev status .. UBUNTU /mnt/galaxyTools/galaxy-central $ hg summary parent: 8116:ecd131b136d0 tip libraries: fix in query for 'datasets_are_public' branch: default commit: 2 modified, 268 unknown update: (current) This is a poor fault report but .. appreciate any pointers here. Many thanks ... -- Greg Edwards, Port Jackson Bioinformatics gedwards2(a)gmail.com

2 1

April 8, 2013 Galaxy Security Release
by Nate Coraor 08 Apr '13

08 Apr '13

A security vulnerability was recently discovered that would allow a malicious person to delete the contents of a history that does not belong to them. The vulnerability was in a method designed to allow users to switch between histories as a convenience from certain messages and is not used for most normal history switching operations. A fix has been provided in the stable branch of the Galaxy distribution and tagged as security_2013.04.08. Administrators are strongly encouraged to upgrade to at least the listed tag or to implement one of the provided workarounds. This changeset *is not* included in the most recent (April 1, 2013) stable release. To upgrade: % hg pull % hg update security_2013.04.08 For Galaxy installations on relatively old versions that administrators are not yet ready to upgrade, there are two workarounds. First, the patch can be downloaded and applied manually: % wget -o history.patch https://bitbucket.org/galaxy/galaxy-central/commits/883216b2eaf2ff05b7771f4… and then: % hg patch history.patch or: % patch -p1 < history.patch In this case, the Galaxy server process(es) must be restarted for the change to take effect. Second, access to this method via the upstream proxy server can be denied. Note that anyone with the ability to bypass the proxy server via directly connecting to the Galaxy application's web port(s) would still be able to call this method. This is possible for anyone with direct login access to the server, or even remotely if the Galaxy application binds to all addresses (instead of just localhost) unless restricted by other means (e.g. a firewall). For Apache: <Location ~ "/history/switch_to_history.*"> Deny from all </Location> For nginx: location ~ /history/switch_to_history.* { deny all; } If using a proxy prefix (e.g. "/galaxy"), that prefix should be prepended to "/history". --nate Galaxy Team

1 0

Pgp Keys not found error nebc.nerc.ac.uk
by Zeeshan Ali Shah 08 Apr '13

08 Apr '13

I am getting this when install I tried to serach the following keys on other server but could not find it on other pgp key server Err http://nebc.nerc.ac.uk unstable Release.gpg Unable to connect to nebc.nerc.ac.uk:http: Ign http://nebc.nerc.ac.uk unstable Release Ign http://nebc.nerc.ac.uk unstable/bio-linux TranslationIndex Err http://nebc.nerc.ac.uk unstable/bio-linux amd64 Packages Unable to connect to nebc.nerc.ac.uk:http: Err http://nebc.nerc.ac.uk unstable/bio-linux i386 Packages Unable to connect to nebc.nerc.ac.uk:http: Err http://nebc.nerc.ac.uk unstable/bio-linux Translation-en_US Unable to connect to nebc.nerc.ac.uk:http: Err http://nebc.nerc.ac.uk unstable/bio-linux Translation-en Unable to connect to nebc.nerc.ac.uk:http: Ign http://downloads-distro.mongodb.org dist/10gen Translation-en Fetched 316 B in 3s (99 B/s) W: There is no public key available for the following key IDs: 3B4FE6ACC0B21F32 W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 759A8E0E5BA15160 W: There is no public key available for the following key IDs: 3B4FE6ACC0B21F32 W: There is no public key available for the following key IDs: 3B4FE6ACC0B21F32 W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/Release.gpg Unable to connect to nebc.nerc.ac.uk:http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-amd64/Pack… Unable to connect to nebc.nerc.ac.uk: http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/Packa… Unable to connect to nebc.nerc.ac.uk: http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/i18n/Translation-… Unable to connect to nebc.nerc.ac.uk: http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/i18n/Translation-… Unable to connect to nebc.nerc.ac.uk: http: -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah

3 2

Galaxy dont work on my Bio-Linux
by BrozPetr＠email.cz 08 Apr '13

08 Apr '13

Hello, please could you help me, how to run galaxy directly from my computer? I am using Bio-Linux (ubuntu distribution) and there is GALAXY already install. When I try to open it, it is state that: "The Galaxy server doesn't seem to be running on your machine. You may need to start it with the command: sudo start galaxy Or else Galaxy may still be starting up (it takes a couple of minutes to get going on the first run)." When I open terminal and write sudo start galaxy it is state that galaxy start/running... But when I trying to open galaxy (just double clic on the icon) it still state problem which I write above. Could you help me please how to fix it?? Thank you very much for your reply! Have a nice day, Petr.

2 1

Re: [galaxy-dev] REST API: upload of dataset to history possible ?
by John Chilton 08 Apr '13

08 Apr '13

On Mon, Apr 8, 2013 at 7:58 AM, Marc Logghe <Marc.Logghe(a)ablynx.com> wrote: > YES!!! > I really could not have found that by myself. Thank you very much. > Great, I am re-responding to galaxy-dev just in case someone else has this problem. > BTW: I have made some additions to blend4j in order to make it compatible to Richard Park's REST API changes regarding the passing of tool parameters. Are these the changes that have made it into Galaxy? If so, if you send me a patch or pull request I would be happy to review it for inclusion into blend4j. Thanks for using blend4j! -John > It allows to pass parameters like this: > WorkflowInputs inputs = new WorkflowInputs(); > inputs.setDestination(new WorkflowInputs.ExistingHistory(history.getId())); > inputs.setWorkflowId(projectWorkflow.getId()); > // Set parameters for params2yaml tool > inputs.setParameters("params2yaml", new ToolParameters("project", "APR000200")); > > Not entirely satisfied with it; might need some api changes but was kind of POC. I also would need some more info from Richard because it is not clear to me if his REST API adjustments allow for multiple parameters. > > Cheers, > Marc > > -----Original Message----- > From: jmchilton(a)gmail.com [mailto:jmchilton@gmail.com] On Behalf Of John Chilton > Sent: Monday, April 08, 2013 2:50 PM > To: Marc Logghe > Subject: Re: [galaxy-dev] REST API: upload of dataset to history possible ? > > Can you retry that with "?" as the db key, admittedly that could use > some more documentation :). The db key is the short identifier > associated with the genome corresponding to the data, "?" indicates > none is specified. > > -John > > On Sun, Apr 7, 2013 at 2:06 PM, Marc Logghe <Marc.Logghe(a)ablynx.com> wrote: >> Thanks John. >> Not sure what I am doing wrong, but in my hands it does not work. No errors but there is no file upload either. >> >> ToolsClient toolsClient = galaxyInstance.getToolsClient(); >> ClientResponse result = toolsClient.fileUploadRequest(history.getId(), "txt", "whatIsAdbKey?", new File("C:\\Users\\mlogghe\\Documents\\bb3d562ec52a9fc5.yml")); >> System.out.println(result.getClientResponseStatus()); >> >> In paster.log I also do not see any evidence that upload_handler is called. >> >> Regards, >> Marc >> >> -----Original Message----- >> From: jmchilton(a)gmail.com [mailto:jmchilton@gmail.com] On Behalf Of John Chilton >> Sent: Thursday, April 04, 2013 3:40 PM >> To: Marc Logghe >> Cc: galaxy-dev(a)lists.bx.psu.edu >> Subject: Re: [galaxy-dev] REST API: upload of dataset to history possible ? >> >> On Tue, Apr 2, 2013 at 5:23 AM, Marc Logghe <Marc.Logghe(a)ablynx.com> wrote: >>> Hi, >>> >>> Is it currently possible to upload an input dataset to a history via the >>> REST API ? >> >> This has been possible since pull request 94: >> https://bitbucket.org/galaxy/galaxy-central/pull-request/94/enable-upload-o…. >> The idea is to use the tools API and to invoke the upload1 tool. I >> imagine this is a little tricky to do with the bioblend Python library >> right now, but the blend4j Java library has a high-level helper >> function (ToolsClient.fileUploadRequest) to make this pretty simple: >> >> https://github.com/jmchilton/blend4j/blob/master/src/main/java/com/github/j… >> >> -John >> >> >>> Or should one use a library dataset instead ? >>> >>> But in the latter case, only an admin can upload data, right ? >>> >>> >>> >>> Thanks, >>> >>> Marc >>> >>> ________________________________________ >>> THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY >>> TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, >>> CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. >>> If the reader of this E-mail message is not the intended recipient, you are >>> hereby notified that any dissemination, distribution or copying of this >>> communication is strictly prohibited. If you have received this >>> communication in error, please notify us immediately at ablynx(a)ablynx.com. >>> Thank you for your co-operation. >>> "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. >>> ________________________________________ >>> >>> >>> ___________________________________________________________ >>> 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/ >> ________________________________________ >> THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. >> If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. >> "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. >> ________________________________________ >> >> >> ___________________________________________________________ >> 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/ > ________________________________________ > THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. > If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. > "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. > ________________________________________ >

1 0

How to show alert message to user when running a tool in galaxy
by BingXin Lu 08 Apr '13

08 Apr '13

Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure that there are no conflict records in the database. So sometimes an alert message should be sent to user if there are wrong records in the database. But I have not found out an efficient way to implement this in galaxy. I am wondering if it is possible to give some warning message to users when running a tool in galaxy and how to do it if it is feasible. I implemented the tool with an xml file and a python file. I am wondering calling javascript from the python code to give user error information. But it seems infeasible and I do not know where to start. Do you have any ideas? Thank you very much! Best regards, --Bingxin

2 2

REST API: upload of dataset to history possible ?
by Marc Logghe 07 Apr '13

07 Apr '13

Hi, Is it currently possible to upload an input dataset to a history via the REST API ? Or should one use a library dataset instead ? But in the latter case, only an admin can upload data, right ? Thanks, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________

3 3