Re: [galaxy-dev] Galaxy behind a authenticated proxy Server
Hi You do not specify which proxy server it is, for example MS TMG ( CNTLM auth ) / Squid. For CNTLM based authentication you could make use of the CNTLM application in most repositories to run a local proxy instance and configure your galaxy user environment with http_proxy=http://localhost:8080. This is only if you need specific stuff you would like your galaxy environment to make use of. For squid you could make use of other methods. However, if you are navigating via the Get Data section, BioMart Central Server, your authenticated browser will retrieve the data of the BioMart server into iframe. Hope this helps. Cheers On 13/08/2013 11:16, Jurgens de Bruin wrote: To All, I am in the process of setting-up a local galaxy server. To access the internet we are required to go trough a authenticated proxy server before any web-services can be accessed. So my questions is how will galaxy handle this? -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/?? Jurgens de Bruin ___ 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/ ___ 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
Peter, Björn, The August Galaxy release is out, and the template_command is now in the stable repository and branch. Regarding matplotlib and numpy, I currently only see matplotlib depending on the 74c21f9bdc39 revision of numpy. Is this still an issue, or has it been resolved? --Dave B. On 8/12/13 11:36:00.000, Bjoern Gruening wrote: On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote: Maybe I should retitle this thread... On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Thank you - installing the NumPy package now works for me, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 I'm moving on to something odd with matplotlib instead... Peter There are currently two revisions to the main Tool Shed package for numpy, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 Rev 0: c75482be1d3a - needs not-yet-released features Rev 1: 74c21f9bdc39 - simplified I'm trying to install a package dependent on this via matplotlib - but installing the matplotlib package fails: http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2 This is something odd, why does it think it needs to install the rev 0 c75482be1d3a version of package_numpy_1_7? See screenshot, except here: Repository dependencies - installation of these additional repositories is required Name RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc Uninstalled Yes, the matplotlib tool_dependencies.xml does list the original revision: package name=numpy version=1.7.1 repository changeset_revision=c75482be1d3a name=package_numpy_1_7 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package package name=freetype version=2.4.11 repository changeset_revision=8761091302c4 name=package_freetype_2_4 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package But I thought as a Tool dependency definition only the tip revision is ever used? That is also what I understood, regardless of the revision there is only one install able revision. But I guess the TS is generating the path to numpy from the package tag and that points to an old non existing version. Hmm. Something for Greg to look at then. After attempting to install this, the status is Installed, missing repository dependencies and this oddity about wanting two revisions of NumPy persists. The actual failure appears to be in compiling matplotlib itself... I don't think it is finding the NumPy installation. Is it possible to view the INSTALLATION.log from within the Galaxy Admin web interface? Yes you should see all installed files/folder and the INSTALLATION.log in your web browser. Can you give me a little more information on how to see this from within Galaxy? 1. Open my Galaxy instance and log in, 2. Click on Admin from top menu 3. Click on Manage installed tool shed repositories on left 4. Select repository of interest 5. Click, Manage tool dependencies 6. Choose one of the dependencies There should be a tree like structure to navigate to your INSTALLATION.log file besides your env.sh file. At this point the repository drop down menus I see are Get updates and Delete or inactivate. I must be looking in the wrong place? I can reproduce it here and it fails because of numpy. OK, that's good - it sounds like the rival revision problem is what is going wrong. One fix to get it working is to upload again biopython. Good plan - as discussed here: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016001.html Done. Thank you, Peter ___ 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/ ___ 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
On Tue, Aug 13, 2013 at 2:01 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, Björn, The August Galaxy release is out, and the template_command is now in the stable repository and branch. Regarding matplotlib and numpy, I currently only see matplotlib depending on the 74c21f9bdc39 revision of numpy. Is this still an issue, or has it been resolved? --Dave B. Thanks Dave, In the short term simplifying the NumPy package then (in a cascade) updating other packages dependent on that new latest revision was enough to get the packages I was testing to install on the July stable release. Updating to the new August stable release should hopefully fix some/all of the issues we were struggling with - if there are any still outstanding we will let you know. The sooner the Tool Shed starts testing package installation the better though - for example this would have caught the template_command problem much quicker (using a new unreleased feature on the main Tool Shed): https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages Cheers, Peter ___ 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/
[galaxy-dev] Running Jobs:
Hey All, Apologies for all the questions on the mailing list...I am having a lot of difficulty getting our local Galaxy working. Currently I have galaxy running but when I try run a job it just stays on Job is waiting to run and never runs. I have read the guide and wiki but can't seem to solve my problem at all... The output of sh run.sh: sh run.sh /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * python path is: /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/boto-2.5.2-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Whoosh-0.3.18-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/amqplib-0.6.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pexpect-2.4-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Babel-0.9.4-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Mako-0.4.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/WebHelpers-0.2-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/WebOb-0.8.5-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Routes-1.12.3-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/wchartype-0.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/elementtree-1.2.6_20050316-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/docutils-0.7-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/PasteDeploy-1.5.0-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Paste-1.7.5.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/lib, /scratch/sysusers/galaxy/galaxy_env/lib64/python26.zip, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/plat-linux2, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-tk, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-old, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-dynload, /usr/lib64/python2.6, /usr/lib/python2.6, /scratch/sysusers/galaxy/galaxy_env/lib/python2.6/site-packages /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://user:pass@host/dbname Starting server in PID 59419. serving on 0.0.0.0:8989 view at http://127.0.0.1:8989 /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927: SAWarning: The IN-predicate on request_type.id was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 155.240.187.100 - - [13/Aug/2013:12:28:36 +] GET /root HTTP/1.1 200 - - Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 155.240.187.100 - - [13/Aug/2013:12:28:37 +] GET /root/welcome HTTP/1.1 302 - http://155.240.187.2:8989/root; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 155.240.187.100 - - [13/Aug/2013:12:28:37 +] GET /history HTTP/1.1 200 - http://155.240.187.2:8989/root; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 155.240.187.100 - - [13/Aug/2013:12:28:37 +] GET /history/get_display_application_links HTTP/1.1 200 - http://155.240.187.2:8989/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101
[galaxy-dev] Help with cluster setup
I am totally lost on what is happening now, I have Galaxy running but jobs
are not being run:
This is my setup:
torque:
qmgr -c 'p s'
#
# Create queues and set their attributes.
#
#
# Create and define queue batch
#
create queue batch
set queue batch queue_type = Execution
set queue batch resources_default.nodes = 1
set queue batch resources_default.walltime = 01:00:00
set queue batch enabled = True
set queue batch started = True
#
# Set server attributes.
#
set server scheduling = True
set server acl_hosts = manager
set server managers = root@*
set server managers += jurgens@*
set server operators = galaxy@*
set server operators += jurgens@*
set server operators += root@*
set server default_queue = batch
set server log_events = 511
set server mail_from = adm
set server scheduler_iteration = 600
set server node_check_rate = 150
set server tcp_timeout = 300
set server job_stat_rate = 45
set server poll_jobs = True
set server mom_job_sync = True
set server keep_completed = 300
set server next_job_number = 17
set server moab_array_compatible = True
This is my job_conf.xml
?xml version=1.0?
!-- A sample job config that explicitly configures job running the way it
is configured by default (if there is no explicit config). --
job_conf
plugins
!-- plugin id=drmaa type=runner
load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=4/ --
plugin id=drmaa type=runner
load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/
/plugins
handlers default=batch
handler id=cn01 tags=batch/
handler id=cn02 tags=batch/
/handlers
destinations default=batch
destination id=batch runner=drmaa tag=cluster,batch
param id=nativeSpecfication-q batch/param
/destination
/destinations
/job_conf
This is parts of the universe_wsgi.ini
# Configuration of the internal HTTP server.
[server:main]
# The internal HTTP server to use. Currently only Paste is provided. This
# option is required.
use = egg:Paste#http
# The port on which to listen.
port = 8989
# The address on which to listen. By default, only listen to localhost
(Galaxy
# will not be accessible over the network). Use '0.0.0.0' to listen on all
# available network interfaces.
#host = 127.0.0.1
host = 0.0.0.0
# Use a threadpool for the web server instead of creating a thread for each
# request.
use_threadpool = True
# Number of threads in the web server thread pool.
#threadpool_workers = 10
# Set the number of seconds a thread can work before you should kill it
(assuming it will never finish) to 3 hours.
threadpool_kill_thread_limit = 10800
[server:cn01]
use = egg:Paste#http
port = 8090
host = 127.0.0.1
use_threadpool = true
threadpool_worker = 5
[server:cn02]
use = egg:Paste#http
port = 8091
host = 127.0.0.1
use_threadpool = true
threadpool_worker = 5
Where cn01 and cn02 are cluster nodes
echo $DRMAA_LIBRARY_PATH
/usr/local/lib/libdrmaa.so
On 8 August 2013 16:58, Nate Coraor n...@bx.psu.edu javascript:_e({},
'cvml', 'n...@bx.psu.edu'); wrote:
On Aug 7, 2013, at 9:23 PM, shenwiyn wrote:
Yes,and I also have the same confuse about that.Actually when I set
server:id in the universe_wsgi.ini as follows for a try,my Galaxy doesn't
work with Cluster,if I remove server:id,it work .
Hi Shenwiyn,
Are you starting all of the servers that you have defined in
universe_wsgi.ini? If using run.sh, setting GALAXY_RUN_ALL in the
environment will do this for you:
http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
[server:node01]
use = egg:Paste#http
port = 8080
host = 0.0.0.0
use_threadpool = true
threadpool_workers = 5
This is my job_conf.xml :
?xml version=1.0?
job_conf
plugins workers=4
plugin id=local type=runner
load=galaxy.jobs.runners.local:LocalJobRunner workers=4/
plugin id=pbs type=runner
load=galaxy.jobs.runners.pbs:PBSJobRunner workers=8/
/plugins
handlers default=batch
handler id=node01 tags=batch/
handler id=node02 tags=batch/
/handlers
destinations default=regularjobs
destination id=local runner=local/
destination id=regularjobs runner=pbs tags=cluster
param
id=Resource_Listwalltime=24:00:00,nodes=1:ppn=4,mem=10G/param
param
id=galaxy_external_runjob_scriptscripts/drmaa_external_runner.py/param
param
id=galaxy_external_killjob_scriptscripts/drmaa_external_killer.py/param
param
id=galaxy_external_chown_scriptscripts/external_chown_script.py/param
/destination
/destinations
/job_conf
The galaxy_external_* options are only supported with the drmaa plugin,
and actually only belong in the univese_wsgi.ini for the moment, they have
not been migrated to the new-style job configuration. They should also
only be used if you are attempting to set up run jobs as the real user
job running capabilities.
Further more when I want to kill my jobs by clicking
Re: [galaxy-dev] Cloudman could not determine the version of Tophat and cufflinks.
I think you are experiencing this bug, which is a major problem with the latest AMI. https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to-mnt From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Anto Praveen Rajkumar Rajamani [a...@hum-gen.au.dk] Sent: Tuesday, August 13, 2013 4:05 AM To: cleme...@galaxyproject.org Cc: galaxy-...@bx.psu.edu Subject: [galaxy-dev] Cloudman could not determine the version of Tophat and cufflinks. Hello, Along with the Tophat (could not determine version: http://dev.list.galaxyproject.org/Problems-with-Tophat-amp-uploading-files-to-Cloudman-by-FTP-td4661119.html) problem in my cloudman, I experience a similar problem with Cufflinks. I uploaded a trial BAM file and ran cufflinks 0.0.6. The run failed and I got a message that Could not determine the version of Cufflinks. When I tried to report the bug using the green bug icon, I get a message Mail is not configured to report this bug. I updated my Galaxy to http://bit.ly/galaxy20130812 and restarted my instance. My instance is on, but I am unable to analyse my data. Where do I go wrong? Kindly help me to solve this problem. Thank you. Best wishes, Anto ___ 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/
[galaxy-dev] Join the HOMER Galaxy wrapper development!
Hi Galaxy Tool developers! I have started to integrate the HOMER suite into Galaxy. My initial attempt can be found here: https://github.com/bgruening/galaxytools/tree/master/homer Currently, we make use of: - Tool Shed definitions of all required 3rd Party Software - datatype definitions - loc files to define different HOMER datasets - macros - compostite datatypes (html output) I think that project can be a good start to learn Galaxy Tool development with all its simple and enhanced features. Also HOMER is a complex suite and you can add small and really big features if you like. If you are interested but did not have any experience in Tool development, do not hesitate to ask. I will try to help and explain as much as I can. For the beginning I included only 3 tools, and only one of them with a bunch of parameters. So there are many things to do ... If anyone is interested in leaning Galaxy Tool development and want to contribute. Fell free to join and contact me. Cheers, Bjoern P.S. I do not mind to merge my changes to the already existing repository from Kevin, but I was not able to contact him. http://toolshed.g2.bx.psu.edu/view/kevyin/homer ___ 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/
Re: [galaxy-dev] Action type 'template_command' on galaxy-dist?
Hi Dave, for us I think everything is fixed. But we had a bad bug in the 'single revision' implementation of the new 'Tool dependency definition' type. We had something like that: A (tool dependency definition) - B (tool) - C (workflow) We changed A (that was numpy) and thought it would be ok to install the workflow afterwards. Because, if A has only one revision associated than it should be working. But B had a reference to the old revision of A (in the XML file) which causes an error. Or the TS wanted to install two different versions of A. Our fix was to upload B again and than C, to renew the revision tags. That was more a hack than a solution :) I do not know if that still occurs with the latest version of galaxy, we tested it with the old stable version. Thanks, Bjoern Peter, Björn, The August Galaxy release is out, and the template_command is now in the stable repository and branch. Regarding matplotlib and numpy, I currently only see matplotlib depending on the 74c21f9bdc39 revision of numpy. Is this still an issue, or has it been resolved? --Dave B. On 8/12/13 11:36:00.000, Bjoern Gruening wrote: On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote: Maybe I should retitle this thread... On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Thank you - installing the NumPy package now works for me, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 I'm moving on to something odd with matplotlib instead... Peter There are currently two revisions to the main Tool Shed package for numpy, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 Rev 0: c75482be1d3a - needs not-yet-released features Rev 1: 74c21f9bdc39 - simplified I'm trying to install a package dependent on this via matplotlib - but installing the matplotlib package fails: http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2 This is something odd, why does it think it needs to install the rev 0 c75482be1d3a version of package_numpy_1_7? See screenshot, except here: Repository dependencies - installation of these additional repositories is required Name RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc Uninstalled Yes, the matplotlib tool_dependencies.xml does list the original revision: package name=numpy version=1.7.1 repository changeset_revision=c75482be1d3a name=package_numpy_1_7 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package package name=freetype version=2.4.11 repository changeset_revision=8761091302c4 name=package_freetype_2_4 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package But I thought as a Tool dependency definition only the tip revision is ever used? That is also what I understood, regardless of the revision there is only one install able revision. But I guess the TS is generating the path to numpy from the package tag and that points to an old non existing version. Hmm. Something for Greg to look at then. After attempting to install this, the status is Installed, missing repository dependencies and this oddity about wanting two revisions of NumPy persists. The actual failure appears to be in compiling matplotlib itself... I don't think it is finding the NumPy installation. Is it possible to view the INSTALLATION.log from within the Galaxy Admin web interface? Yes you should see all installed files/folder and the INSTALLATION.log in your web browser. Can you give me a little more information on how to see this from within Galaxy? 1. Open my Galaxy instance and log in, 2. Click on Admin from top menu 3. Click on Manage installed tool shed repositories on left 4. Select repository of interest 5. Click, Manage tool dependencies 6. Choose one of the dependencies There should be a tree like structure to navigate to your INSTALLATION.log file besides your env.sh file. At this point the repository drop down menus I see are Get updates and Delete or inactivate. I must be looking in the wrong place? I can reproduce it here and it fails because of numpy. OK, that's good - it sounds like the rival revision problem is what is going wrong. One fix to get it working is to upload again biopython. Good plan - as discussed here: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016001.html Done. Thank you, Peter ___ Please keep all replies on the list by using reply all in
Re: [galaxy-dev] Cloudman could not determine the version of Tophat and cufflinks.
Thank you for the reply. I do not have any working knowledge of ubuntu and linux commands. Moreover, I work from a windows computer. I can see that this problem is being discussed since July12th http://dev.list.galaxyproject.org/Cloudman-Software-does-not-work-due-to-broken-symlinks-td4660619.html When will this bug be solved? I terminated my cloudman instance with frustration. Anto Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. E-mail: a...@hum-gen.au.dk From: Ravpreet Setia [ravpreet.se...@oicr.on.ca] Sent: 13 August 2013 17:02 To: Anto Praveen Rajkumar Rajamani; cleme...@galaxyproject.org Cc: galaxy-...@bx.psu.edu Subject: RE: [galaxy-dev] Cloudman could not determine the version of Tophat and cufflinks. I think you are experiencing this bug, which is a major problem with the latest AMI. https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to-mnt From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Anto Praveen Rajkumar Rajamani [a...@hum-gen.au.dk] Sent: Tuesday, August 13, 2013 4:05 AM To: cleme...@galaxyproject.org Cc: galaxy-...@bx.psu.edu Subject: [galaxy-dev] Cloudman could not determine the version of Tophat and cufflinks. Hello, Along with the Tophat (could not determine version: http://dev.list.galaxyproject.org/Problems-with-Tophat-amp-uploading-files-to-Cloudman-by-FTP-td4661119.html) problem in my cloudman, I experience a similar problem with Cufflinks. I uploaded a trial BAM file and ran cufflinks 0.0.6. The run failed and I got a message that Could not determine the version of Cufflinks. When I tried to report the bug using the green bug icon, I get a message Mail is not configured to report this bug. I updated my Galaxy to http://bit.ly/galaxy20130812 and restarted my instance. My instance is on, but I am unable to analyse my data. Where do I go wrong? Kindly help me to solve this problem. Thank you. Best wishes, Anto ___ 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/
[galaxy-dev] ENA galaxy import link broken?
Hello, I am trying to use the ENA galaxy import feature. This involves going to the analyze menu in galaxy and clicking the link 'EBI SRA' which is encoded as http://www.ebi.ac.uk/ena/data/search?GALAXY_URL=https%3A//main.g2.bx.psu.edu/tool_runner%3Ftool_id%3Debi_sra_main This does not seem to be working at present. I manage a Galaxy site that uses a similar setup encoded as (also doesn't work) http://www.ebi.ac.uk/ena/data/search?GALAXY_URL=http%3A//rnaseq.pathogenportal.org/tool_runner%3Ftool_id%3Debi_sra_main I sent an email off to ENA but haven't got a response. Any ideas? Thanks for any help, Andrew Warren ___ 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/
[galaxy-dev] adding reference genome
Dear sir, please add reference genome of Zebra finch genome in Bowtie2 and Tophat2 option in galaxy. thank u ___ 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/
[galaxy-dev] outputs label attribute
Dear all, I have managed to use something like outputs data format=fasta name=output label=#echo os.path.splitext (str ($input.name))[0]#-ORF.fasta/ /outputs to display the wanted label for the dataset in the history. However when I applied the same code to other tool wrappers, some weird things happened: the wrapper can still be loaded in the web page, but when I click the execute button to submit the job, nothing happened except the web browser giving the status wait for localhost. I cannot think of any reason for that. The main difference I can think of between the successful wrapper and the failed ones is that in the failed ones I have to do some file manipulations as galaxy always stores its dataset with the file suffix .dat which is not acceptable in the tool, e.g. proteowizard. I have to rename it with the correct suffix and move the final result to the output file. Additional related questions: 1. How to display the selected value of a conditional element in the label? $conditional.value? 2. How to display different strings according to the conditional selection? Similar to command element to use #if #elsif #end if? 3. When usingdata name=output format=csv change_format when input=type value=html format=html/ /change_format /data, could I use label attribute in the data and when elements? Look forward to your kind answers. Many thanks in advance. Best regards! Jun ___ 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/
Re: [galaxy-dev] adding reference genome
Hi Vijay, For right now, using a Custom reference genome with these tools is the best solution: http://wiki.galaxyproject.org/Support#Custom_reference_genome This genome in Galaxy is sourced from UCSC, as you probably know: http://wiki.galaxyproject.org/Support#Reference_genomes The longer-term strategy for new/updated indexes will be worked out soon. Our immediate goal was to get the tools out on Main as soon as possible. Thanks, Jen Galaxy team On 8/13/13 1:20 PM, Vijay Kumar wrote: Dear sir, please add reference genome of Zebra finch genome in Bowtie2 and Tophat2 option in galaxy. thank u ___ 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/
[galaxy-dev] how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini
Hi Tin, I am going to move this over to the galaxy-...@bx.psu.edu mailing list (good for local install questions) to give it better viability. I am by no means the best person to help with this, so hopefully others will jump in, but just from looking at this I am wondering if you shouldn't be instead looking at the job_conf.xml.sample_advanced file. There is the default version as well, but it is probably not what you are looking for if you want to add custom logging scripts. For universe_wsgi.ini, it seems like maybe the problem with the syntax is most likely the unknown default_cluster_job_runner variable and the double = in the line. Slashes should be fine unescaped here. But as I said, I think the other file is the place for the changes anyway, or maybe both, but using known variables and a single = per path. But let's see what the developers think! Jen Galaxy team On 8/12/13 3:49 PM, tin h wrote: Hello galaxy gurus, I am trying to configure a local galaxy server to submit to SGE using DRMAA, it works, but I would like to specify the equivalent of -v TMPDIR=/scratch for qsub. I tried updating universe_wsgi.ini with something like:  default_cluster_job_runner =  drmaa://-q default.q -V -v TMPDIR=/scratch/ but that doesn't work because / is a delimiter, and I have not been able to find way to escape it.  Is there any tricks for this? Much thanks in advance for your help in this matter. -Tin ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/
