Re: [galaxy-dev] reload a tool's configuration from command line
Hi Jan This is brilliant - it is always the simple solutions you overlook - thank you very much! May I just add a modified version, in case you use external authentication. There is no point to create a cookie, since you need to provide userid (not the e-mail) and password each time. So a simple line using the '-u' option will do: curl --silent --data-ascii tool_id=my_toolreload_tool_button=Reload -u userid: http://mygalaxy.ch/admin/reload_tool Thanks again, Hans On 03/27/2012 11:27 AM, Haarst, Jan van wrote: I just did a test, and this works : First login, so you get your login cookie : curl --cookie-jar galaxy_cookie.txt --data-ascii 'email=jan.vanhaarst%40wur.nlwebapp=galaxypassword=geheimlogin_button=Login' http://dev1.ab.wurnet.nl:8086/user/login Then use that cookie to login, and reload your tool: curl --silent --cookie galaxy_cookie.txt --data-ascii tool_id=sffinforeload_tool_button=Reload http://dev1.ab.wurnet.nl:8086/admin/reload_tool | grep donemessage If all went well, you get this back : div class=donemessageReloaded the tool:br/bname:/b sffinfobr/bid:/b sffinfobr/bversion:/b 1/div HTH, Jan -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev- boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: maandag 26 maart 2012 17:22 To: Tim-Christoph Roloff Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] reload a tool's configuration from command line On Mar 22, 2012, at 11:28 AM, Tim-Christoph Roloff wrote: Hello, I was wondering if there is a way to trigger the reload of a tool's configuration from command line. We are using a tool that loads .xml files from tool-data. The .xml files get modified by a script ran by cron frequently. Right now we reload the tool config via the admin interface but ideally we could integrate the reload in the cron job. Best regards Tim Hi Tim, A few people have done it by creating a script that acts as a web client and performs the function via the web interface. There's no direct way to do it from the command line without restarting the server, unfortunately. --nate ___ 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/ ___ 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/
Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
Hi Robert Have you looked at the Download or Export option? - you get this option, when you click on the triangle next to the names of you workflows. Regards, Hans On 03/27/2012 08:36 PM, Robert Chase wrote: Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab ___ 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/ ___ 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/
[galaxy-dev] Local galaxy cannot connect to local toolshed
Hi, I managed to run a local Tool Shed and add a repository. On the same machine, a local galaxy is running, and configured for using this local toolshed. In the Admin menu of Galaxy, I can see my local Toolshed listed under 'Search and Browse tool sheds'. However, when I click on my local toolshed entry, following connection error appears in the main window: This webpage is not available The webpage at*http://localhost:9009/repository/browse_valid_repositories?galaxy_url=http://192.168.10.24/webapp=galaxy*might be temporarily down or it may have moved permanently to a new web address. Here are some suggestions: * Reload http://localhost:9009/repository/browse_valid_repositories?galaxy_url=http://192.168.10.24/webapp=galaxythis web page later. Error 102 (net::ERR_CONNECTION_REFUSED): The server refused the connection. Thanks for the help, Joachim Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/
Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever
Dear Galaxy Dev,
Now I have another problem with the Galaxy sample tracking data
transfer. Galaxy is not able to transfer the datasets but when it
attempts to associate the datasets with the library and folder
specified in the sequencing request I get this:
2012-03-28 13:07:02,706 - datatx_18327 - Setting status Adding to
data library for dataset All of sample 16
2012-03-28 13:07:02,706 - datatx_18327 -
(u'c969d2e16ec64867a127d6e3a4018b12',
u'http://galaxydev/api/samples/1e8ab44153008be8',
{'sample_dataset_ids': ['2f94e8ae9edff68a', '8237ee2988567c1c'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-28 13:07:02,817 - datatx_18327 - [200, 'Done']
2012-03-28 13:07:02,818 - datatx_18327 -
(u'c969d2e16ec64867a127d6e3a4018b12',
u'http://galaxydev/api/libraries/1e8ab44153008be8/contents',
{'file_type': 'auto', 'server_dir':
'/gpfshpc/data/pmrdcdb/galaxy/datatx_18327_28Mar2012', 'dbkey': '',
'create_type': 'file', 'folder_id':
'994debf9f6ab02b99d7cff57c04c6b7c', 'upload_option':
'upload_directory'})
2012-03-28 13:07:02,906 - datatx_18327 - 400 Bad Request
The server could not comply with the request since
it is either malformed or otherwise incorrect.
Malformed LibraryFolder id ( 994debf9f6ab02b99d7cff57c04c6b7c )
specified, unable to decode
What could be the problem here? Any help would be appreciated.
regards,
Leandro
On Wed, Mar 28, 2012 at 1:15 PM, Leandro Hermida
soft...@leandrohermida.com wrote:
Dear Galaxy Dev,
Ok I have gotten further found out what was going on, in my
data_transfer.log I was getting HTTP 404 Not Authorized when the data
transfer was trying to access Galaxy API URLs
http://galaxyserver/api/... This is because we are using external user
authentication as documented in
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
all of Galaxy behind this authentication. Since the Galaxy API uses
API keys to essentially authenticate you have to change you Location
/ ... /Location container to not match URLs starting with /api. To
do this you have to change it to LocationMatch ^/(?!api)
/LocationMatch.
best,
leandro
On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang yangl...@isu.edu wrote:
I've got the same problem and when I looked at the data_transfer.log, I saw
the following message:
2012-03-01 15:12:27,338 - datatx_13870 -
(u'9c17d84742cd2acb63d88b5bd41d968f',
u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
{'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-01 15:12:27,342 - datatx_13870 - Error. !DOCTYPE HTML PUBLIC
-//IETF//DTD HTML 2.0//EN
htmlhead
title405 Method Not Allowed/title
/headbody
h1Method Not Allowed/h1
pThe requested method PUT is not allowed for the URL
/api/samples/2d9035b3fc152403./p
hr
Using Galaxy instead of Apache as the web server changed the sample status
from in queue to complete but didn't add the downloaded files to the data
library.
Luobin
On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
soft...@leandrohermida.com wrote:
Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The galaxy_listener.log shows:
2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
{'config_file': 'universe_wsgi.ini', 'http_server_section':
'server:main'}
2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
'rabbitmqctl_path':
'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
'5672'}
2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
127.0.0.1:5672
2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py
data_transfer
galaxy_hostrd-galaxydev.app.pmi/galaxy_host
api_key69bbd1a9b18eda2a888e9963820d8ef0/api_key
data_hostchp723/data_host
data_usergalaxy/data_user
data_passwordmypassword/data_password
request_id12/request_id
sample_id12/sample_id
library_id15/library_id
folder_id52/folder_id dataset
dataset_id10/dataset_id
namettt_2.fastq.gz/name
file/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz/file
/datasetdataset
dataset_id9/dataset_id
namettt_1.fastq.gz/name
file/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz/file
Re: [galaxy-dev] run cluster jobs as real user
Hi, after thinking more about this and also trying to get Apache use NIS (I failed with that :-( ) I just came up with an idea for a different solution: I don't use NIS for login into galaxy but when starting jobs I consult a mapping file (or the database) to map email addresses to know users. For unknown users I just continue to use the galaxy user. I guess a good starting point would be DRMAAJobRunner.queue_job Do you see any bigger problems coming my way? How best do I avoid to degress from the main tree to much? regards, Andreas On 27.03.2012 09:57, Andreas Kuntzagk wrote: Hi, On 26.03.2012 17:14, Nate Coraor wrote: On Mar 22, 2012, at 12:30 PM, Alfonso Núñez Salgado wrote: Hi Andreas: As far as I know Galaxy is designed to manage its own users and not to be integrated in any other platform. I think that the idea is to use galaxy as another user of your system. Hi Alfonso, Andreas is referring to recent changes that allow jobs to run as users other than the single Galaxy user that started the server process. See: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User Yes, that's what I wanted. On 20/03/12 16:31, Andreas Kuntzagk wrote: Hi, I (re-)installed galaxy on our server and managed to set it up to run jobs through our cluster (GridEngine). It's also running behind an Apache proxy now. But now I'm wondering how to setup to have the cluster jobs run as the real cluster users. I found the documentation on this topic a little thin. We use NIS for managing users and passwords across the cluster. How do I connect that to Galaxy? regards, Andreas Andreas, You'll need to have Apache authenticate your users, as explained here: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy For NIS without Kerberos, you'd probably need to use mod_auth_pam to authenticate through your system's PAM stack. Thanks, I will look into it. regards, Andreas --nate -- = Alfonso Núñez Salgado Unidad de Bioinformática Centro de Biologia Molecular Severo Ochoa C/Nicolás Cabrera 1 Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid (Spain) Phone: (34) 91-196-4633 Fax: (34) 91-196-4420 web: http://ub.cbm.uam.es/ = ___ 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/ ___ 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/ -- 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/
Re: [galaxy-dev] Error when installing galaxy
Jemma, It looks like the boto package is not installed on your system. Try: sudo apt-get install python-boto Dave B. On 3/18/12 8:19 PM, Jemma Wu wrote: Dear Galaxy developers, This is the first time that I installed Galaxy on a Debian Lenny 64 bit server. I got an error of “ImportError: No module named boto” when I ran %sh run.sh. Please see the error message of the installation output below: File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 90, in app_factory add_ui_controllers( webapp, app ) File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 39, in add_ui_controllers module = __import__( module_name ) File /home/galaxy/galaxy-dist/lib/galaxy/web/controllers/cloud.py, line 9, in module import boto ImportError: No module named boto Does anyone know how to fix this error? Thanks in advance! Regards, Jemma ___ 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/ ___ 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/
Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever
Dear Galaxy Dev,
The malformed library folder error on the latest galaxy-dist I am
gettting (shown below) right after data transfer I am pretty sure is a
bug and regression.
I was just able to do the exact same sample tracking setup on one of
my other Galaxy servers which is an older galaxy-dist version from
last year and everything works ok during library folder association.
regards,
Leandro
On Wed, Mar 28, 2012 at 1:20 PM, Leandro Hermida
soft...@leandrohermida.com wrote:
Dear Galaxy Dev,
Now I have another problem with the Galaxy sample tracking data
transfer. Galaxy is not able to transfer the datasets but when it
attempts to associate the datasets with the library and folder
specified in the sequencing request I get this:
2012-03-28 13:07:02,706 - datatx_18327 - Setting status Adding to
data library for dataset All of sample 16
2012-03-28 13:07:02,706 - datatx_18327 -
(u'c969d2e16ec64867a127d6e3a4018b12',
u'http://galaxydev/api/samples/1e8ab44153008be8',
{'sample_dataset_ids': ['2f94e8ae9edff68a', '8237ee2988567c1c'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-28 13:07:02,817 - datatx_18327 - [200, 'Done']
2012-03-28 13:07:02,818 - datatx_18327 -
(u'c969d2e16ec64867a127d6e3a4018b12',
u'http://galaxydev/api/libraries/1e8ab44153008be8/contents',
{'file_type': 'auto', 'server_dir':
'/gpfshpc/data/pmrdcdb/galaxy/datatx_18327_28Mar2012', 'dbkey': '',
'create_type': 'file', 'folder_id':
'994debf9f6ab02b99d7cff57c04c6b7c', 'upload_option':
'upload_directory'})
2012-03-28 13:07:02,906 - datatx_18327 - 400 Bad Request
The server could not comply with the request since
it is either malformed or otherwise incorrect.
Malformed LibraryFolder id ( 994debf9f6ab02b99d7cff57c04c6b7c )
specified, unable to decode
What could be the problem here? Any help would be appreciated.
regards,
Leandro
On Wed, Mar 28, 2012 at 1:15 PM, Leandro Hermida
soft...@leandrohermida.com wrote:
Dear Galaxy Dev,
Ok I have gotten further found out what was going on, in my
data_transfer.log I was getting HTTP 404 Not Authorized when the data
transfer was trying to access Galaxy API URLs
http://galaxyserver/api/... This is because we are using external user
authentication as documented in
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
all of Galaxy behind this authentication. Since the Galaxy API uses
API keys to essentially authenticate you have to change you Location
/ ... /Location container to not match URLs starting with /api. To
do this you have to change it to LocationMatch ^/(?!api)
/LocationMatch.
best,
leandro
On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang yangl...@isu.edu wrote:
I've got the same problem and when I looked at the data_transfer.log, I saw
the following message:
2012-03-01 15:12:27,338 - datatx_13870 -
(u'9c17d84742cd2acb63d88b5bd41d968f',
u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
{'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-01 15:12:27,342 - datatx_13870 - Error. !DOCTYPE HTML PUBLIC
-//IETF//DTD HTML 2.0//EN
htmlhead
title405 Method Not Allowed/title
/headbody
h1Method Not Allowed/h1
pThe requested method PUT is not allowed for the URL
/api/samples/2d9035b3fc152403./p
hr
Using Galaxy instead of Apache as the web server changed the sample status
from in queue to complete but didn't add the downloaded files to the data
library.
Luobin
On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
soft...@leandrohermida.com wrote:
Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The galaxy_listener.log shows:
2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
{'config_file': 'universe_wsgi.ini', 'http_server_section':
'server:main'}
2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
'rabbitmqctl_path':
'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
'5672'}
2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
127.0.0.1:5672
2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py
data_transfer
galaxy_hostrd-galaxydev.app.pmi/galaxy_host
Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
Hi Rob I don't know what exactly you mean by new server. Assuming you are just talking about different hardware: Have you considered moving 'everything' to the new server? ie copying the Galaxy directory tree (especially make sure you copy ~/database/ ) and connect to the same PostgreSQL (or MySQL) database. If you want, I can give you more details how we successfully changed the hardware of our server last year Regards, Hans On 03/28/2012 03:31 PM, Robert Chase wrote: Thank you that could be very helpful to our users if we can't download them all as one big batch. I was hoping to be able to do something to save the users the headache of having to export and upload their workflows to the new server. Regards, -Rob On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Robert Have you looked at the Download or Export option? - you get this option, when you click on the triangle next to the names of you workflows. Regards, Hans On 03/27/2012 08:36 PM, Robert Chase wrote: Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab _ 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/ ___ 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/
Re: [galaxy-dev] cluster_files_directory not getting cleaned
Ann, Could you give me the value of the cleanup_jobs configuration entry in universe_wsgi.ini? Thank you, Dave B. On 3/21/12 4:35 PM, Ann Black wrote: Hello - I have noticed on our local install, that the job scripts as well as stdout/err in our cluster_files_directory is not getting cleaned up. When I track the jobs in our runner logs, for a sampling of the job scripts left over in the cluster_files_directory, the jobs are completing out successfully and there are no errors in the log. I have not tried to check if all scripts are not getting cleaned, or just some … but by the volume of them it looks like all of them may not be getting removed/cleaned up after the job completes out. Any thoughts on what may be going on? Thanks, Ann ___ 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/ ___ 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/
Re: [galaxy-dev] Same error in multiple tools
Hi, I'm running these tools on a cluster.. Alban Emil Bouvier wrote: Alban, Are you running these tools on a cluster, or on a local system? Dave B. On 3/19/12 6:55 AM, Alban Lermine wrote: Hi, I have the same error message for multiple tools (GFFtoBED, BEDtoBIGBED,BAMtoSAM,...): /from galaxy import eggs ImportError: No module named galaxy It's happening only since the last upgrade, do you know what is going wrong? Thanks, Alban / -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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/
Re: [galaxy-dev] cluster_files_directory not getting cleaned
Hello - Thanks much for the response. I do not find an entry in my universe_wsgi.ini file for cleanup_jobs - should I have one? Ann On 3/28/12 9:45 AM, Emil Bouvier d...@bx.psu.edu wrote: Ann, Could you give me the value of the cleanup_jobs configuration entry in universe_wsgi.ini? Thank you, Dave B. On 3/21/12 4:35 PM, Ann Black wrote: Hello - I have noticed on our local install, that the job scripts as well as stdout/err in our cluster_files_directory is not getting cleaned up. When I track the jobs in our runner logs, for a sampling of the job scripts left over in the cluster_files_directory, the jobs are completing out successfully and there are no errors in the log. I have not tried to check if all scripts are not getting cleaned, or just some but by the volume of them it looks like all of them may not be getting removed/cleaned up after the job completes out. Any thoughts on what may be going on? Thanks, Ann ___ 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/ ___ 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/
Re: [galaxy-dev] add a tool to galaxy
Hi, Try: --no_overlap $singleOrPair.no_overlap Best, L-A Le 28/03/2012 18:59, cai cai a écrit : Hi All, I am trying to add a tool to Galaxy, here is my xml configuration: ## Set params based on whether reads are single-end or paired. #if $singleOrPair.readType == paired: --no_overlap $singleOrPair.readType.no_overlap #end if conditional name=singleOrPair param name=readType type=select label=single end or paired end reads option value=singlesingle end/option option value=pairedpaired end/option /param when value=paired param name=no_overlap type=select label= option value=nono/option option value=yesyes/option /param /when when value=single / /conditional I met the following error. Could some let me know what is wrong? Thank you very much. Cai Traceback (most recent call last): File /mnt/galaxyTools/galaxy-central/lib/galaxy/jobs/runners/drmaa.py, line 124, in queue_job job_wrapper.prepare() File /mnt/galaxyTools/galaxy-central/lib/galaxy/jobs/__init__.py, line 372, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py, line 1585, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File cheetah_DynamicallyCompiledCheetahTemplate_1332953248_1_41760.py, line 96, in respond *NotFound: cannot find 'no_overlap' while searching for 'singleOrPair.readType.no_overlap'* ___ 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/ ___ 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/
Re: [galaxy-dev] add a tool to galaxy
Thank you very much L-A. It works perfectly. Cai 2012/3/28 Louise-Amélie Schmitt louise-amelie.schm...@embl.de Hi, Try: --no_overlap $singleOrPair.no_overlap Best, L-A Le 28/03/2012 18:59, cai cai a écrit : Hi All, I am trying to add a tool to Galaxy, here is my xml configuration: ## Set params based on whether reads are single-end or paired. #if $singleOrPair.readType == paired: --no_overlap $singleOrPair.readType.no_overlap #end if conditional name=singleOrPair param name=readType type=select label=single end or paired end reads option value=singlesingle end/option option value=pairedpaired end/option /param when value=paired param name=no_overlap type=select label= option value=nono/option option value=yesyes/option /param /when when value=single / /conditional I met the following error. Could some let me know what is wrong? Thank you very much. Cai Traceback (most recent call last): File /mnt/galaxyTools/galaxy-central/lib/galaxy/jobs/runners/drmaa.py, line 124, in queue_job job_wrapper.prepare() File /mnt/galaxyTools/galaxy-central/lib/galaxy/jobs/__init__.py, line 372, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py, line 1585, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File cheetah_DynamicallyCompiledCheetahTemplate_1332953248_1_41760.py, line 96, in respond*NotFound: cannot find 'no_overlap' while searching for 'singleOrPair.readType.no_overlap'* ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
Thank you that could be very helpful to our users if we can't download them all as one big batch. I was hoping to be able to do something to save the users the headache of having to export and upload their workflows to the new server. Regards, -Rob On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Robert Have you looked at the Download or Export option? - you get this option, when you click on the triangle next to the names of you workflows. Regards, Hans On 03/27/2012 08:36 PM, Robert Chase wrote: Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab __**_ 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/ ___ 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/
[galaxy-dev] Custom Get Data page doesn't recognize completion of large file downloads
I have a custom module/page created to get data from some SOAP-based web services. I haven't determined the threshold yet, but for small BAM files, Galaxy behaves just fine. However, when I get large BAM files (I've had the same results with 10gig and 40gig files), Galaxy doesn't recognize when the download is complete. I can look in the /database/files/000 directory and see the download is complete (md5sum confirms it), but Galaxy just keeps on saying Job is currently running. It takes a Galaxy reboot for it to recognize the complete download. Any ideas on how to fix this? Thanks -Brian ___ 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/
[galaxy-dev] toolrunner / xml parse
I am getting an error upon my local Galaxy startup which I suspect is causing an invalid tool runner entry in my left hand menu (my tool url is: http://localhost:8081/tool_runner/index instead of http://localhost:8081/tool_runner?tool_id=FLASHforFASTQ) Here is the error I get: galaxy.tools DEBUG 2012-03-28 13:48:28,658 Loading section: MyTools galaxy.tools DEBUG 2012-03-28 13:48:28,665 Loaded tool: sam_to_bam_QT 0.0.1 galaxy.tools DEBUG 2012-03-28 13:48:28,671 Loaded tool: BAMtoFASTQ 0.01 galaxy.tools.test DEBUG 2012-03-28 13:48:28,677 Error in add_param for readleft: Unable to determine parameter type of test input 'readleft'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2012-03-28 13:48:28,677 Error in add_param for readright: Unable to determine parameter type of test input 'readright'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools DEBUG 2012-03-28 13:48:28,678 Loaded tool: FLASHFASTQ 0.01 Here is the xml for my tool: tool id=FLASHFASTQ name=FLASH Overlap for FASTQ version=0.01 descriptionFinds overlaps between paired fastq files or fills the insert with N's/description command interpreter=python FLASHforFASTQ.py --readleft=$readleft --readright=$readright --output=$output1 /command inputs data format=fastqsanger name=readleft type=data label=Left fastq reads FASTQ files ftype=fastqsanger / data format=fastqsanger name=readright type=data label=Right fastq reads FASTQ files ftype=fastqsanger / /inputs outputs param format=fasta name=output1 type=data label=Overlap sequences in FASTA format/ /outputs tests test !-- FLASH to FASTQ conversion command: /bioinformatics/asm/bio_bin/Galaxy/galaxy-dist/tools/mytools/FLASHforFASTQ.py -lr -rr -output1 -- param name=readleft value=quick-taxa.r1.fastq type=data ftype=fastqsanger / param name=readright value=quick-taxa.r2.fastq type=data ftype=fastqsanger / output name=output1 file=quick-taxa.fasta ftype=fasta / /test /tests help **What it does** This tool uses a modifed version of the FLASH overlapper to overlap paired end reads together and outputs the the resulting sequence in FASTA format /help /tool What's the problem?!?! Daniel Brami Synthetic Genomics, Inc. Senior Research Associate, Bioinformatics 11149 North Torrey Pines Road La Jolla, California 92037 Phone: 858.433.2230 Fax: 858.754.2988 dbr...@syntheticgenomics.commailto:dbr...@syntheticgenomics.com www.SyntheticGenomics.comhttp://www.syntheticgenomics.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: http://lists.bx.psu.edu/
Re: [galaxy-dev] toolrunner / xml parse
That did it! Silly mistake - thanks so much!! -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Wednesday, March 28, 2012 2:21 PM To: Brami, Daniel Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] toolrunner / xml parse data format=fastqsanger name=readleft type=data label=Left fastq reads FASTQ files ftype=fastqsanger / data format=fastqsanger name=readright type=data label=Right fastq reads FASTQ files ftype=fastqsanger / These inputs should be defined using the param tag, and not the data tag. Here's the wiki page with more details: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cparam.3E_tag_set -Dannon ___ 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/
