galaxy-dev April 2012

galaxy-dev@lists.galaxyproject.org

101 participants
198 discussions

Workflow API (runtime modification of tool parameters)
by Richard Park 21 Jun '12

21 Jun '12

Hello, I was wondering what would be the best way to extend Galaxy's API functionality to allow for runtime modification of tool parameters? I have successfully been able to run workflows programmatically using the API, following the basic steps in: scripts/api/execute_workflow.py. scripts/api/example_watch_folder.py However, it is unclear to me, what would be the best way to run workflows through API with specific parameters at various steps. Should I generate new workflows for every workflow that requires different parameters and upload this to galaxy? Or would it be better to extend the API to allow for runtime parameter configuration? If this is the case, any pointers on how to extend this would be greatly appreciated. Thank you, Richard Park

2 7

Configuring Galaxy for FTP upload
by Ciara Ledero 13 Jun '12

13 Jun '12

Hi all, According to Galaxy, uploading files larger than 2GB will surely fail. For this reason, uploading via FTP is recommended. Unfortunately, I cannot download/install an FTP server for Galaxy since I am working on a remote server. I only have access to it via Xming. Is there anyway to allow FTP upload, without using ProFTPd? Can I use Mozilla's fireFTP or Linux's own FTP? (Actually, I tried to connect to Galaxy, but I was denied access.). Thank you in advance for any help. CL

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Galaxy server configuration question
by Huayan Gao 07 Jun '12

07 Jun '12

Dear Sir or Madam, I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? Best, Huayan

4 16

LookupError: No section 'main' (prefixed by 'server') found in config
by Iry Witham 07 Jun '12

07 Jun '12

I have performed a new install of Galaxy for development and deployment purposes. However, when I run the run.sh script I get the following error: Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 274, in command relative_to=base, global_conf=vars) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 308, in loadserver relative_to=relative_to, **kw) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 210, in loadserver return loadobj(SERVER, uri, name=name, **kw) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 363, in get_context object_type, name=name) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 528, in find_config_section self.filename)) LookupError: No section 'main' (prefixed by 'server') found in config /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini I have modified the universe_wsgi.ini to reflect the way our production server is configured. The following is the server section of that file: # # Galaxy is configured by default to be useable in a single-user development # environment. To tune the application for a multi-user production # environment, see the documentation at: # # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer # # Throughout this sample configuration file, except where stated otherwise, # uncommented values override the default if left unset, whereas commented # values are set to the default value. # examples of many of these options are explained in more detail in the wiki: # # Config hackers are encouraged to check there before asking for help. # ---- HTTP Server ---------------------------------------------------------- # Configuration of the internal HTTP server. [server:web0] use = egg:Paste#http port = 8080 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # Configuration of web server 2 [server:web1] use = egg:Paste#http port = 8081 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # Configuration of web server 3 [server:web2] use = egg:Paste#http port = 8082 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # 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 = 8080 # 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 = 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 = 5 # ---- Filters -------------------------------------------------------------- # Filters sit between Galaxy and the HTTP server. # These filters are disabled by default. They can be enabled with # 'filter-with' in the [app:main] section below. # Define the gzip filter. [filter:gzip] use = egg:Paste#gzip # Define the proxy-prefix filter. [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy My production server works fine, but this one will not run. What am I missing? Thanks, Iry

3 2

uploading multiple files into one dataset
by Jorrit Boekel 01 Jun '12

01 Jun '12

Dear list, Our lab's proteomics data is frequently outputted into >50 files containing different fractions of proteins. The files are locally stored and not present on the Galaxy server. We've planned to somehow (inside galaxy) merge these files and split them into tasks so they can be run on the cluster. We would either merge/split the files by concatenation, or untar/tar files at every job, depending on filetype and tool. No problems so far. However, I have been looking around for a way to upload >50 files simultaneously to galaxy and convert to one dataset, and this does not seem to be supported. Before starting to create a hack to make this work, which doesn't seem especially trivial to me, I'd like to know if I should instead use libraries. From what I've seen, libraries are not treated as datasets in Galaxy but rather contain datasets. If there was a "tar all sets in library and import to history" I'd be using that, but I've only encountered "tar/zip sets and download locally" which would be a bit of a workaround. I haven't found much on this subject in the mailing list, has this functionality been requested before? cheers, jorrit boekel

2 2

Galaxy administrators - admin_users setting
by Peter Cock 30 May '12

30 May '12

Hi all, To make someone an administrator on a local Galaxy install, do I just need to add their email (login) to the comma separated setting admin_users in universe_wsgi.ini? https://bitbucket.org/galaxy/galaxy-central/wiki/Admin/AdminInterface I have this working on one server, but it doesn't seem to have any effect on a second server. Both are now running the current release (changeset 50e249442c5a). Is there some other setting needed to enable the admin interface? Thanks, Peter

2 4

Batch limit on Wokflows
by Petit III, Robert A. 29 May '12

29 May '12

Hi there, I've run into an issue on my local galaxy install. When I have 20 or more datasets in my history, I no longer get the option to 'Enable/Disable selection of multiple input files...' I instead get a broken drop down list. I say broken because its as though the drop down list and input box have merged together. Is there a setting I need to change to correct this? Thanks Robert ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

4 11

how is metadata generated
by KOH Jia Yu Jayce 28 May '12

28 May '12

Hi Just wondering how metadata files in galaxy-dist/database/files/_metadata_files are generated? Are there any configurations in the xmls that specify these to be generated? Thanks

7 17

debugging jobs in 'new' state
by Shantanu Pavgi 10 May '12

10 May '12

We experienced an issue where some of the galaxy jobs were sitting in the 'new' state for a quite long time. They were not waiting for cluster resources to become available, but haven't been even queued up through DRMAA. We are currently using non-debug mode and following were my observations: * No indication of new jobs in paster.log file * database/pbs script didn't contain any associated job scripts * in backend database - job table contained their galaxy job id but no command_line input was recorded Also, not all the jobs are waiting in the 'new' state. Many jobs submitted after above waiting jobs got completed successfully on the cluster. Is there any job submission logic within galaxy which is being used for submitting jobs? Any clues on how to debug this issue will be really helpful. -- Thanks, Shantanu.

3 4

R scripts for DESeq
by Jennifer Jackson 10 May '12

10 May '12

Hi Lisa, I am going to send your question over to the galaxy-dev(a)bx.psu.edu mailing list so that the development community can offer feedback. http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-cloud… Th galaxy-user list is primarily for tool/data usage on the Galaxy public server. http://wiki.g2.bx.psu.edu/Mailing%20Lists Thanks, Jen Galaxy team -------- Original Message -------- Subject: [galaxy-user] R scripts for DESeq Date: Tue, 21 Feb 2012 23:25:35 -0500 From: Liusong Yang <liusongyang2009(a)gmail.com> To: galaxy-user(a)lists.bx.psu.edu Hello, I am planning to put DESeq into galaxy. I am a newcomer for both Galaxy and R. I have already read all of the related discussion in this group. I also noticed that there are r_wrapper.sh and DESeq.xml added into galaxy recently under the path of tools. These lines are from r_wrapper.sh. ### Run R providing the R script in $1 as standard input and passing ### the remaining arguments on the command line I guess this means we need to give the DESeq R script to the wrapper as standard input. My question is where or what is the DESeq R scripts? I installed R and DESeq package, but I can not fund anything like DESeq.R or something similar? I feel so confusing now. Any comments or suggestions would be absolutely appreciated! Thanks Lisa ___________________________________________________________ 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/

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galaxy-dev April 2012