Re: [galaxy-dev] workflow startup issues
Aside: If I add steps to the beginning of the workfow, the step that runs too early, typically occurs earlier in the flow. Can this indicate a race condition where not all dependencies are available (stored?) yet in the database at the time of querying for job eligible for queueing? Best, Geert On 05/21/2013 11:06 PM, Geert Vandeweyer wrote: Hi Dannon, I pulled the new updates and restarted galaxy. However, the issue is not resolved. Is there other information you might need? hg summary: parent: 9332:0f51ae4f1c84 tip Unicode fixes for workflow names in Tool Menu. branch: stable Best, Geert On 05/21/2013 06:08 PM, Dannon Baker wrote: Ok, so you're running the old tip of -dist. There are a few new updates you can retrieve using `hg pull -u -b stable http://bitbucket.org/galaxy/galaxy-central` http://bitbucket.org/galaxy/galaxy-central%60. -Dannon On Tue, May 21, 2013 at 12:01 PM, Geert Vandeweyer geert.vandewey...@ua.ac.be mailto:geert.vandewey...@ua.ac.be wrote: hg summary: parent: 9320:47ddf167c9f1 tip Use Galaxy's ErrorMiddleware since Paste's doesn't return start_response. Fixes downloading tarballs from the Tool Shed when use_debug = false. branch: stable commit: 18 modified, 178 unknown update: (current) Geert On 05/21/2013 04:59 PM, Dannon Baker wrote: Geert, This should be fixed in the up-to-date stable branch as far as I know. Can you tell me what 'hg summary' states? -Dannon On Mon, May 20, 2013 at 4:43 PM, Geert Vandeweyer geert.vandewey...@ua.ac.be mailto:geert.vandewey...@ua.ac.be wrote: Hi, After the latest upgrade (april), I'm having issues when starting (batch) workfows. Sometimes, it seems that step dependencies are not stored correctly, leading to some steps being started too soon, without prior datasets being completed. Specifically, for some workflows, some of the later steps start immediately. The issue seems to be random: in batch workflow submission, some run flawlessly, others show the issue, at different steps. I use one handler in the job_conf to exclude race conditions and shared variable clashes. I suspect there is an issue with fetching or storing the steps to/from the database (a remote mysql database in my case). On the mysql-side there are no errors in the log files, and the galaxy-logs don't show clear issues either. Does the job new job handler check for failed database connections? If not, could somebody point me to the code that performs these steps, I'd like to add a check retry routine to see if this improves the situation. best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be mailto:geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail:geert.vandewe...@ua.ac.be mailto:geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail:geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ Please keep all replies on the list by using
Re: [galaxy-dev] import Workflow from public Galaxy to local instance
Hi, On 21.05.2013 18:06, Dannon Baker wrote: This interaction is pretty clunky right now (I've made a trello card for improving it: https://trello.com/c/eu8XiJLK. Two options right now are: 1) Import (on main) each workflow you want to copy to your local instance, and generate the regular download link for import. (Download or Export in the workflow menu, once you've imported it) I wanted to avoid that since I have to import more then one workflow. 2) Munge the URLs yourself -- all accessible workflows are available for download via https://main.g2.bx.psu.edu/workflow/export_to_file?id=workflow_id But how do I get the workflow_id? For example for the workflow https://main.g2.bx.psu.edu/u/gm2123/w/cloudmap-unmapped-mutant-workflow-no-candidates what would the workflow_id be? (I tried cloudmap-unmapped-mutant-workflow-no-candidates but this did not work.) regards, Andreas -Dannon On Tue, May 21, 2013 at 11:56 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de mailto:andreas.kuntz...@mdc-berlin.de wrote: Hi, I want to make workflows published on usegalaxy.org http://usegalaxy.org available for users on our local instance. How do I do this? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/__bimsb/BIMSB_groups/Dieterich http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich _ 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/ http://galaxyproject.org/search/mailinglists/ -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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] import Workflow from public Galaxy to local instance
On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: But how do I get the workflow_id? For example for the workflow https://main.g2.bx.psu.edu/u/**gm2123/w/cloudmap-unmapped-** mutant-workflow-no-candidateshttps://main.g2.bx.psu.edu/u/gm2123/w/cloudmap-unmapped-mutant-workflow-no-candidates what would the workflow_id be? (I tried cloudmap-unmapped-mutant-**workflow-no-candidates but this did not work.) If you click on that link above, you can see the id in the url for the 'Import' link. Again, definitely not optimal -- public workflows should probably all be exposed via the API for use/import. ___ 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] location of .loc-files/data tables -- bug or feature?
Hey Dannon, thnx for the info and the quick reply! On 21.05.2013 18:09, Dannon Baker wrote: Hey Christian, This is a bug that surfaced in revision 8333 which should be fixed in 9326:d07c62f0067a, which is available in the most recent galaxy-dist (stable branch). If you'd rather not update right away, we'll have another full-fledged dist release out soon. -Dannon On Tue, May 21, 2013 at 5:48 AM, Christian Hundsrucker christian.hundsruc...@ur.de mailto:christian.hundsruc...@ur.de wrote: Hello, Galaxy developers! I do a bit of tweaking to a local galaxy instance. Thus, I just realized that subdirectories are not supported for the location of .loc-files/data tables. E.g. tool-data/somesub/my.loc is not recognized even if this location is correctly linked in the tool_data_table_conf.xml (file path=tool-data/somesub/my.loc /). Via the Galaxy-Admin interface and 'Server', 'View data tables registry' the .loc file is marked as a Missing index file - in the example the displayed location would be tool-data/my.loc (without the 'somesub' subdirectory). As soon as I store 'my.loc' directly in the tool-data directory galaxy runs smoothly again, even (!) if I keep the subdirectory in the file path in tool_data_table_conf.xml. Is galaxy meant to behave like this? If so, a word about it in the documentation would be really helpful! Best, Christian version: changeset: 8796:961ae35ba612 branch: stable tag: tip parent: 8794:1c7174911392 user:Nate Coraor n...@bx.psu.edu mailto:n...@bx.psu.edu date:Fri Feb 08 11:23:04 2013 -0500 ___ 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/ ___ 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] Samtools and idxstats
Hi, I would like to inquire whether anyone has attempted to implement the idxstats tool from samtools into Galaxy? The xml-file for idxstats is not present in the Galaxy source code, which led me to try and implement it myself. However, the main problem I face is that the idxstats tool silently relies on having an index file available (within the same directory) for the bam file you which to print the stats for. E.g. samtools idxstats PATH/test.bam searches for PATH/test.bam.bai and gives an error when this file is not present. And somehow I cannot model this behavior in Galaxy. A different solution would of course be to ask the author(s) of samtools to have an option available where the user can directly indicate the path to the index file. regards, Michiel PS: I've searched the mailing list archives for this problem but did not find any matches. Apologies if I somehow missed the answer. -- == Michiel Van Bel, PhD Expert Bioinformatician Tel:+32 (0)9 331 36 95fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mi...@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be == ___ 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] Problem with ftp connexion to Galaxy
Hello, I am a new Galaxy User. I am definitely not an expert in informatics, so my questions may sound silly to you... I apologize if it is the case! Anyway, I cound not establish a ftp connexion to Galaxy through Filezilla, and the error message suggests that it comes from an incorrect password to Galaxy. Here is the messages displayed by Filezilla (french version) while trying to connnect: Statut :Résolution de l'adresse de main.g2.bx.psu.edu Statut :Connexion à 128.118.250.4:21... Statut :Connexion établie, attente du message d'accueil... Réponse : 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP) [:::128.118.250.4] Commande : USER fbesn...@biologie.ens.fr Réponse : 331 Password required for fbesn...@biologie.ens.fr Commande : PASS *** Réponse : 530 Login incorrect. Erreur :Erreur critique Erreur :Impossible d'établir une connexion au serveur I was puzzled by this error message, because I do connect as user in the Galaxy website. As recommended, I use the SAME login (=email adress)/Password in both Galaxy login page and filezilla. I tried to reset my password and connect again: I could connect directly to the web site, but I still failed establishing a connexion via filezilla. I just created an account yesterday to Galaxy (Tuesday, 21th of May 2013). Maybe I should just wait a little bit for a synchronization of the user connexion parameters, should I? Moreover, my Filezilla is working with other ftp server, so that I think we can exclude that the problem comes from there. I extensively looked for similar trouble reports on internet (googling with other terms 530 Login incorrect). Unfortunately, I could not solve this problem. However, I found that you were asked one year ago for a similar problem in this page: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-July/010457.html But I must confess that I could not understand most of what was written in this informatic experts discussion! By the way, my system is not an ubuntu, so I think that the solution you suggested would not work in my case. Here are the characteristics and versions of the systems installed on my computer: Operating system: Windows 7 professionnal, 64bits Filezilla Client 3.7.0.1 Firefox 20.0.1 I really thank you for reading this help message and I hope that you could explain me how to solve my problem. I look forward to reading your answer soon, Best regards, -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesn...@biologie.ens.fr Tel: +33-1-44-32-39-44 ___ 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] Samtools and idxstats
Galaxy stores a BAI for each BAM internally; you can access it in a tool
wrapper like this (assuming the name of your input dataset is 'input_bam':
${input_bam.metadata.bam_index}
Once you have the file path, you can set up a symbolic link to it and the tool
should work fine.
Good luck,
J.
On May 22, 2013, at 4:05 AM, Michiel Van Bel wrote:
Hi,
I would like to inquire whether anyone has attempted to implement the
idxstats tool from samtools into Galaxy?
The xml-file for idxstats is not present in the Galaxy source code, which led
me to try and implement it myself.
However, the main problem I face is that the idxstats tool silently relies on
having an index file available (within the same directory) for the bam file
you which to print the stats for.
E.g. samtools idxstats PATH/test.bam
searches for PATH/test.bam.bai and gives an error when this file is not
present. And somehow I cannot model this behavior in Galaxy.
A different solution would of course be to ask the author(s) of samtools to
have an option available where the user can directly indicate the path to the
index file.
regards,
Michiel
PS: I've searched the mailing list archives for this problem but did not find
any matches. Apologies if I somehow missed the answer.
--
==
Michiel Van Bel, PhD
Expert Bioinformatician
Tel:+32 (0)9 331 36 95fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
mi...@psb.vib-ugent.be http://www.psb.vib-ugent.be
http://bioinformatics.psb.ugent.be
==
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[galaxy-dev] nginx Proxy to VM problem
Hey everyone,
I'm having a weird login problem (think it's cookie related) after setting up
Galaxy on a virtual machine and trying to proxy_pass to it using nginx. It says
I'm logged in, but when I get redirected to the front page I'm no longer logged
in. When I visit subsequent pages I'm also not logged in.
On the server, here is the relevant part of my nginx configuration (I'm going
to setup static serving after I get the login issue resolved):
upstream galaxy_app {
server 192.168.1.11:8080;
}
server {
...
location /galaxy {
proxy_pass http://galaxy_app;
proxy_set_header X-Forwarded-Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
}
...
}
The dots just mean that I have other things in there for the forwarding I do
with other VMs.
On the VM, in my universe_wsgi.ini file, I have made sure to set the following
(just showing the parts I think are relevant):
[server:main]
port = 8080
host = 0.0.0.0
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy
[app:main]
filter-with = proxy-prefix
cookie_path = /galaxy
I should note that I might end up changing this configuration to use a CNAME at
some point (thus avoiding the prefix issue), but for now I'm totally lost as to
why I'm not able to login using my current configuration.
Any ideas?
Thanks!
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/
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Re: [galaxy-dev] nginx Proxy to VM problem
I actually fixed the problem by not setting the cookie prefix in the ini file.
Weird.
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/
On Wednesday, May 22, 2013 at 9:51 AM, Michael E. Cotterell wrote:
Hey everyone,
I'm having a weird login problem (think it's cookie related) after setting up
Galaxy on a virtual machine and trying to proxy_pass to it using nginx. It
says I'm logged in, but when I get redirected to the front page I'm no longer
logged in. When I visit subsequent pages I'm also not logged in.
On the server, here is the relevant part of my nginx configuration (I'm going
to setup static serving after I get the login issue resolved):
upstream galaxy_app {
server 192.168.1.11:8080;
}
server {
...
location /galaxy {
proxy_pass http://galaxy_app;
proxy_set_header X-Forwarded-Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
}
...
}
The dots just mean that I have other things in there for the forwarding I do
with other VMs.
On the VM, in my universe_wsgi.ini file, I have made sure to set the
following (just showing the parts I think are relevant):
[server:main]
port = 8080
host = 0.0.0.0
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy
[app:main]
filter-with = proxy-prefix
cookie_path = /galaxy
I should note that I might end up changing this configuration to use a CNAME
at some point (thus avoiding the prefix issue), but for now I'm totally lost
as to why I'm not able to login using my current configuration.
Any ideas?
Thanks!
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/
___
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:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] nginx Proxy to VM problem
That's not the only thing I changed. I also have the following in my nginx conf
file:
proxy_set_header Host $host;
instead of X-Forwarded-Host $host
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/
On Wednesday, May 22, 2013 at 11:11 AM, Michael E. Cotterell wrote:
I actually fixed the problem by not setting the cookie prefix in the ini
file. Weird.
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/
On Wednesday, May 22, 2013 at 9:51 AM, Michael E. Cotterell wrote:
Hey everyone,
I'm having a weird login problem (think it's cookie related) after setting
up Galaxy on a virtual machine and trying to proxy_pass to it using nginx.
It says I'm logged in, but when I get redirected to the front page I'm no
longer logged in. When I visit subsequent pages I'm also not logged in.
On the server, here is the relevant part of my nginx configuration (I'm
going to setup static serving after I get the login issue resolved):
upstream galaxy_app {
server 192.168.1.11:8080;
}
server {
...
location /galaxy {
proxy_pass http://galaxy_app;
proxy_set_header X-Forwarded-Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
}
...
}
The dots just mean that I have other things in there for the forwarding I
do with other VMs.
On the VM, in my universe_wsgi.ini file, I have made sure to set the
following (just showing the parts I think are relevant):
[server:main]
port = 8080
host = 0.0.0.0
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy
[app:main]
filter-with = proxy-prefix
cookie_path = /galaxy
I should note that I might end up changing this configuration to use a
CNAME at some point (thus avoiding the prefix issue), but for now I'm
totally lost as to why I'm not able to login using my current configuration.
Any ideas?
Thanks!
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/
___
Please keep all replies on the list by using reply all
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
[galaxy-dev] command tag in xml file for a C++ tool
Hi all, I want to include a new tool to galaxy. The tool is written in C++. How do I write the xml file to execute a cpp program? The tool that I am trying to integrate ishttps://code.google.com/p/bedtools/ I have the class file to be executed and the command to execute it. For example, 'IntersectBed' is my class file. The command to execute it is $intersectBed -a reads.bed -b genes.bed (reads.bed and genes.bed are input files provided by the user) How should I write the command tag in the xml file so as to execute the above command? Since C++ is complied as opposed to Python which is interpreted, I am not sure how to write the command tag. I am a newbie. I appreciate any guidance offered! Thanks, VJ. ___ 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] command tag in xml file for a C++ tool
On Wed, May 22, 2013 at 5:21 PM, vijayalakshmi v...@buffalo.edu wrote: Hi all, I want to include a new tool to galaxy. The tool is written in C++. How do I write the xml file to execute a cpp program? The tool that I am trying to integrate ishttps://code.google.com/p/bedtools/ I have the class file to be executed and the command to execute it. For example, 'IntersectBed' is my class file. The command to execute it is $intersectBed -a reads.bed -b genes.bed (reads.bed and genes.bed are input files provided by the user) How should I write the command tag in the xml file so as to execute the above command? Since C++ is complied as opposed to Python which is interpreted, I am not sure how to write the command tag. I am a newbie. I appreciate any guidance offered! Thanks, VJ. For a compiled binary there is no interpreter, just use command. e.g. commandIntersectBed -a $inputreads -b $inputgenes .../command I presume there are more options to your command, e.g. output files ;) 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/
Re: [galaxy-dev] command tag in xml file for a C++ tool
You might find it instructive to look at the existing bedtools wrappers here: http://toolshed.g2.bx.psu.edu/view/aaronquinlan/bedtools -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, May 22, 2013 at 12:21 PM, vijayalakshmi v...@buffalo.edu wrote: Hi all, I want to include a new tool to galaxy. The tool is written in C++. How do I write the xml file to execute a cpp program? The tool that I am trying to integrate ishttps://code.google.com/p/bedtools/ I have the class file to be executed and the command to execute it. For example, 'IntersectBed' is my class file. The command to execute it is $intersectBed -a reads.bed -b genes.bed (reads.bed and genes.bed are input files provided by the user) How should I write the command tag in the xml file so as to execute the above command? Since C++ is complied as opposed to Python which is interpreted, I am not sure how to write the command tag. I am a newbie. I appreciate any guidance offered! Thanks, VJ. ___ 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/
[galaxy-dev] populating the pull-down menu: reference genomes (built-in index)
Hi, We are trying to put a few reference genomes into the built-in index for bwa, bowtie, bowtie2 and tophat. For the human hg19 we can find those. However, we also like to upload the Rhesus macaque genome and haven't been able to find an indexed version at NCBI or other places. Are other genomes pre-indexed for these applications somewhere? How do those files look like exactly (extensions, number of files needed, etc.)? How would we index the Rhesus genome for the above mappers if they are not available in an indexed form? Thank you, Jeannette CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. ___ 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] Missing test results on (Test) Tool Shed
Peter, I have implemented a system that will explicitly exclude a defined list of repositories from the testing framework, so your repositories' tests should now be running. --Dave B. On 5/21/13 06:26:56.000, Peter Cock wrote: On Mon, May 13, 2013 at 11:09 AM, Peter Cock p.j.a.c...@googlemail.com wrote: I remain puzzled why I am seeing seemingly stochastic missing test results. Hi Dave, This continues - although I have been making progress with the tests for some of my tools. Currently there are a number of repositories reported as failing but I can't see the error (and so can't do much about fixing it): http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus When previously visible this was due to a test framework limitation testing with composite output files: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014365.html Given I suspect a cache issue hiding the test failures, it might help if rather than the current text like Time tested: ~ 8 hours ago this could also state the date and time of the test (in UTC/GMT to avoid locale confusion). Thanks, Peter Other repositories failing with a clear error message: http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp Missing dependencies, should have been skipped, see http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014748.html http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler Limitation of test framework, Trello issue open for this, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014366.html http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename Limitation of test framework, issue raised, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list Missing an R/Bioconductor dependency, best practise for handling this has yet to be agreed. ___ 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] Test Tool Shed still running tests marked as skip?
Peter, Thank you for reporting this issue, it has been resolved in 9827:2a630237801f. --Dave B. On 5/21/13 06:10:34.000, Peter Cock wrote: Hi Greg, There may be an issue with the new feature to mark a specific revision to skip tool tests. I ticked this earlier this week on this repository, yet the tests appear to have been run overnight (and failed as expected): http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/2b35b5c4b7f4 Revision: 18:2b35b5c4b7f4 Regards, 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] Missing test results on (Test) Tool Shed
On Wed, May 22, 2013 at 6:47 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I have implemented a system that will explicitly exclude a defined list of repositories from the testing framework, so your repositories' tests should now be running. --Dave B. Looks good - and now I have some more errors to sort out :) 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/
Re: [galaxy-dev] Cross Tool Shed dependencies / blast_datatypes
On Mon, May 20, 2013 at 3:05 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, May 20, 2013 at 2:47 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter wrote: Right now the single biggest class of test failures amongst my tools on the Test Tool Shed is a missing dependencies on the blast_datatypes repository: http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes As a short term measure, could the dev team upload blast_datatypes to the Test Tool Shed as well please (and give me write access)? Then thanks to the recent change in [1] I can reference the dependency without explicitly naming the Tool Shed. I've copied the blast_datatypes from the main tool shed to the test tool shed with all history in tact. See http://testtoolshed.g2.bx.psu.edu/view/devteam/blast_datatypes If you can do it in a way that preserves the same revision history can change set hashes even better - then I can replace this: repository toolshed=http://toolshed.g2.bx.psu.edu; name=blast_datatypes owner=devteam changeset_revision=f9a7783ed7b6 / with: repository name=blast_datatypes owner=devteam changeset_revision=f9a7783ed7b6 / and can use the same repository_dependencies.xml file on both Tool Sheds. Great, I'm trying that now here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/9ef0d4ecb9d5 http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bf634ebee84c http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/2d4757de6180 Hi Greg ( Dave), Thanks for Dave for fixing the missing test results issue, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014791.html I can now see the effect the dependency change had - unfortunately the blast_datatypes install seems to be unsuccessful, but I am not seeing a helpful error from the Tool Shed tests. Let's focus on the simplest case, where blast_datatypes is the only dependency: ?xml version=1.0? repositories description=This requires the BLAST datatype definitions (e.g. the BLAST XML format). !-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which added BLAST databases -- repository name=blast_datatypes owner=devteam changeset_revision=f9a7783ed7b6 / /repositories http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bf634ebee84c Automated tool test results Tool test resultshttp://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=doneid=90191ce08fa7fc29message=changeset_revision=bf634ebee84c Automated test environmenthttp://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=doneid=90191ce08fa7fc29message=changeset_revision=bf634ebee84c *Time tested:* ~ 6 hours ago*System:* Linux 3.5.0-21-generic*Architecture:* x86_64*Python version:* 2.7.3*Galaxy revision:* 9821:feaab01c738a*Galaxy database version:* 115*Tool shed revision:* 9820:f5fe2f094060*Tool shed database version:* 19*Tool shed mercurial version:* 2.2.3 Installation errors* - no functional tests were run for any tools in this changeset revision*http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=doneid=90191ce08fa7fc29message=changeset_revision=bf634ebee84c Repository dependencieshttp://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=doneid=90191ce08fa7fc29message=changeset_revision=bf634ebee84c Tool shedNameOwnerChangeset revisiontesttoolshed.g2.bx.psu.edu blastxml_to_top_descrpeterjcbf634ebee84cErrorNone It seems that an error occurred with the dependencies, but unfortunately all we get as the error message is None. Regards, 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/
Re: [galaxy-dev] Cross Tool Shed dependencies / blast_datatypes
I cannot guarantee it, but this may be related to a fix I just committed that populates the repository tag in the dependency definitions with a toolshed attribute if it is missing (it looks like it is in your case). I used to not populate the tag, but simply stored the tool shed in the repository metadata. Bjorn discovered, however, that certain repository installations would not succeed if the toolshed attribute was missing. WHen I investigated this, I discovered that some downstream stuff could not locate the appropriate tool shed if the attribute was missing from the tag. I fixed this in 9836:252027d00b44 by populating this tag attribute if it was missing. Unfortunately, a new dependency definition has to be uploaded to those repositories that have definitions where it is not set in order to get this fix. I don't know if updating your dependency file in this repository will fix this issue, but just wanted to alert you to this. Very sorry for any inconvenience! Greg Von Kuster On May 22, 2013, at 4:26 PM, Peter Cock wrote: On Mon, May 20, 2013 at 3:05 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, May 20, 2013 at 2:47 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter wrote: Right now the single biggest class of test failures amongst my tools on the Test Tool Shed is a missing dependencies on the blast_datatypes repository: http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes As a short term measure, could the dev team upload blast_datatypes to the Test Tool Shed as well please (and give me write access)? Then thanks to the recent change in [1] I can reference the dependency without explicitly naming the Tool Shed. I've copied the blast_datatypes from the main tool shed to the test tool shed with all history in tact. See http://testtoolshed.g2.bx.psu.edu/view/devteam/blast_datatypes If you can do it in a way that preserves the same revision history can change set hashes even better - then I can replace this: repository toolshed=http://toolshed.g2.bx.psu.edu; name=blast_datatypes owner=devteam changeset_revision=f9a7783ed7b6 / with: repository name=blast_datatypes owner=devteam changeset_revision=f9a7783ed7b6 / and can use the same repository_dependencies.xml file on both Tool Sheds. Great, I'm trying that now here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/9ef0d4ecb9d5 http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bf634ebee84c http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/2d4757de6180 Hi Greg ( Dave), Thanks for Dave for fixing the missing test results issue, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014791.html I can now see the effect the dependency change had - unfortunately the blast_datatypes install seems to be unsuccessful, but I am not seeing a helpful error from the Tool Shed tests. Let's focus on the simplest case, where blast_datatypes is the only dependency: ?xml version=1.0? repositories description=This requires the BLAST datatype definitions (e.g. the BLAST XML format). !-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which added BLAST databases -- repository name=blast_datatypes owner=devteam changeset_revision=f9a7783ed7b6 / /repositories http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bf634ebee84c Automated tool test results Tool test results Automated test environment Time tested: ~ 6 hours ago System: Linux 3.5.0-21-generic Architecture: x86_64 Python version: 2.7.3 Galaxy revision: 9821:feaab01c738a Galaxy database version: 115 Tool shed revision: 9820:f5fe2f094060 Tool shed database version: 19 Tool shed mercurial version: 2.2.3 Installation errors - no functional tests were run for any tools in this changeset revision Repository dependencies Tool shed NameOwner Changeset revision testtoolshed.g2.bx.psu.edu blastxml_to_top_descr peterjc bf634ebee84c Error None It seems that an error occurred with the dependencies, but unfortunately all we get as the error message is None. Regards, 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/
[galaxy-dev] Run galaxy on a specific SGE queue
Hi everyone, Galaxy is set up on our cluster, and so far everything is working just fine. However, we'd like to change the submission queue from the default to a specific one. To do so, we tryed to set on the universe_wsgi.ini file the default_cluster_job_runner parameter as following: default_cluster_job_runner = drmaa://-q test.q -l mem=8G -l h_vmem=10G/ When doing so, an error occured telling us the job has been rejected because 2 queues were specified: the workq (default one) and the test.q. Should be the queue setting this way ? What are we doing wrong ? thanks for your help, Sarah -- Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 ___ 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] writing command tag in xml file for a C++ tool
Hi all, I want to include a new tool to galaxy. The tool is written in C++. How do I write the xml file to execute a cpp program? The tool that I am trying to integrate ishttps://code.google.com/p/bedtools/ I have the class file to be executed and the command to execute it. For example, 'IntersectBed' is my class file. The command to execute it is $intersectBed -a reads.bed -b genes.bed (reads.bed and genes.bed are input files provided by the user) How should I write the command tag in the xml file so as to execute the above command? Since C++ is complied as opposed to Python which is interpreted, I am not sure how to write the command tag. I am a newbie. I appreciate any guidance offered! Thanks, VJ. ___ 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] Hard time getting UCSC to work with our server
I'm having a pretty torrid time with this because we've had to implement active
directory authentication for Apache. It works and users can log in with their
AD accounts and that is all fine. The problems arise when I try and get UCSC
to pick up a BAM file. The first problem is that although the Galaxy server is
configured to for UCSC as a display server, putting the following into the
Apache conf as recommended here
http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy doesn't work.
1 Location /root/display_as
2 Satisfy Any
3 Order deny,allow
4 Deny from all
5 Allow from hgw1.cse.ucsc.edu
6 Allow from hgw2.cse.ucsc.edu
7 Allow from hgw3.cse.ucsc.edu
8 Allow from hgw4.cse.ucsc.edu
9 Allow from hgw5.cse.ucsc.edu
10 Allow from hgw6.cse.ucsc.edu
11 Allow from hgw7.cse.ucsc.edu
12 Allow from hgw8.cse.ucsc.edu
13 /Location
All that happens is you get 401 Authorization Required errors indicating that
the Apache server isn't letting the UCSC servers non-authenticated access.
Now, if I add the Allow from hgw etc into the Location / block then it gets
through and then I hit the next problem which is that although I've mapped some
read data against dm3 I'm getting failures inside Galaxy itself related to
serving the bai file UCSC is requesting. Here's the galaxy_access log:
192.168.240.21 - shane [23/May/2013:15:22:24 +1200] GET
/display_application/d3a4d6a5256f2d9a/ucsc_bam/main HTTP/1.1 302 406
hgw4.cse.ucsc.edu - - [23/May/2013:15:22:24 +1200] GET
/dataset/display_application?app_action=paramuser_id=207edd50b8d72f8bapp_name=ucsc_bamaction_param=tracklink_name=maindataset_id=d3a4d6a5256f2d9a
HTTP/1.0 200 311
hgw4.cse.ucsc.edu - - [23/May/2013:15:22:29 +1200] HEAD
/dataset/display_application?app_action=datauser_id=207edd50b8d72f8bapp_name=ucsc_bamaction_param=galaxy_d3a4d6a5256f2d9a.bamlink_name=maindataset_id=d3a4d6a5256f2d9a
HTTP/1.0 200 -
hgw4.cse.ucsc.edu - - [23/May/2013:15:22:31 +1200] HEAD
/dataset/display_application?app_action=datauser_id=207edd50b8d72f8bapp_name=ucsc_bamaction_param=galaxy_d3a4d6a5256f2d9a.bamlink_name=maindataset_id=d3a4d6a5256f2d9a.bai
HTTP/1.0 500 -
hgw4.cse.ucsc.edu - - [23/May/2013:15:22:30 +1200] GET
/dataset/display_application?app_action=datauser_id=207edd50b8d72f8bapp_name=ucsc_bamaction_param=galaxy_d3a4d6a5256f2d9a.bamlink_name=maindataset_id=d3a4d6a5256f2d9a
HTTP/1.0 200 472000
Note the 500 when requesting the bai file.
This is what my manager.log is showing when this happens.
128.114.119.134 - - [23/May/2013:15:22:29 +1300] HEAD
/dataset/display_application?app_action=datauser_id=207edd50b8d72f8bapp_name=ucsc_bamaction_param=galaxy_d3a4d6a5256f2d9a.bamlink_name=maindataset_id=d3a4d6a5256f2d9a
HTTP/1.1 200 3301004 - genome.ucsc.edu/net.c
Exception happened during processing of request from ('127.0.0.1', 60484)
Traceback (most recent call last):
File
/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py,
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib64/python2.6/SocketServer.py, line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib64/python2.6/SocketServer.py, line 618, in __init__
self.finish()
File /usr/lib64/python2.6/SocketServer.py, line 661, in finish
self.wfile.flush()
File /usr/lib64/python2.6/socket.py, line 303, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
128.114.119.134 - - [23/May/2013:15:22:30 +1300] GET
/dataset/display_application?app_action=datauser_id=207edd50b8d72f8bapp_name=ucsc_bamaction_param=galaxy_d3a4d6a5256f2d9a.bamlink_name=maindataset_id=d3a4d6a5256f2d9a
HTTP/1.1 200 3301004 - genome.ucsc.edu/net.c
128.114.119.134 - - [23/May/2013:15:22:31 +1300] HEAD
/dataset/display_application?app_action=datauser_id=207edd50b8d72f8bapp_name=ucsc_bamaction_param=galaxy_d3a4d6a5256f2d9a.bamlink_name=maindataset_id=d3a4d6a5256f2d9a.bai
HTTP/1.1 500 - - genome.ucsc.edu/net.c
Error - type 'exceptions.TypeError': Non-hexadecimal digit found
Exception happened during processing of request from ('127.0.0.1', 60486)
Traceback (most recent call last):
File
/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py,
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib64/python2.6/SocketServer.py, line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib64/python2.6/SocketServer.py, line 618, in __init__
self.finish()
File /usr/lib64/python2.6/SocketServer.py, line 661, in finish
self.wfile.flush()
File /usr/lib64/python2.6/socket.py, line 303, in flush
self._sock.sendall(buffer(data, write_offset,
[galaxy-dev] Workflow refresh
Hi, I upload files which then automatically call execute_workflow.py. The files background turn to green , but to see the workflow running on the GUI I need to refresh the display. Does anyone know how I can add a refresh command to the code, and where in the code to add it. Thanks Neil ___ 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/
