Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of galaxy-dev-requ...@lists.bx.psu.edu [galaxy-dev-requ...@lists.bx.psu.edu] Sent: Saturday, July 07, 2012 11:00 AM To: galaxy-dev@lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 73, Issue 10 Send galaxy-dev mailing list submissions to galaxy-dev@lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-ow...@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than Re: Contents of galaxy-dev digest... HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from Galaxy-dev Digest Vol ... to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. pbs_python issues (Iry Witham) 2. Which css file does welcome.html use? (Dorset, Daniel C) 3. Re: Which css file does welcome.html use? (Jeremy Goecks) Hi Ira, I'm in charge of a Galaxy instance that's also deployed on a PBS Cluster, and I went through this process a couple of months ago. If I remember correctly, when you run your Python script, you're supposed to run it with -e not ?e Assuming that you are pointing to the correct directory, it looks like everything else about your command is correct. Have you tried that? -- Message: 1 Date: Fri, 6 Jul 2012 16:32:14 + From: Iry Witham iry.wit...@jax.org To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] pbs_python issues Message-ID: cc1c8b4d.8ead%iry.wit...@jax.org Content-Type: text/plain; charset=windows-1252 I am having an issue with pbs_python loading, but not submitting jobs to the cluster. The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py ?e pbs_python' it failed to generate the pbs_python egg in the /galaxy-dist/eggs/ directory. Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from my production galaxy server and restarted my test server. It appears to start, but when I attempt to run anything it uses the local runner and fails. The runner0.log shows the pbsjobrunner is loaded is below: galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner: galaxy.jobs.runners.pbs:PBSJobRunner galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue started galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue started galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue started galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue started I can't seem to get past this point since I upgraded. Can someone point me in the right direction? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. -- next part -- An HTML attachment was scrubbed... URL: http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120706/a179a808/attachment-0001.html -- Message: 2 Date: Fri, 6 Jul 2012 16:28:08 -0500 From: Dorset, Daniel C daniel.dor...@vanderbilt.edu To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Which css file does welcome.html use? Message-ID: 9b568b41976b54469cc6e3fd758ef83105dc006...@its-drwnem10.ds.vanderbilt.edu Content-Type: text/plain; charset=us-ascii OK, this is ostensibly a simple question. However, I can't find the CSS file that welcome.html is using. In the HTML file, there's this line: link rel=stylesheet href=style/base.css type=text/css / However, I don't see a directory named style anywhere in the galaxy directory tree. When I search for base.css, from the root Galaxy installation directory, I get the following results: ./static/june_2007_style/blue/base.css ./static/light_hatched_style/blue/base.css ./static/light_hatched_style/green/base.css ./static/old_blue_style/base.css So I assume that one of these is being used? I do think it's strange though, that the HTML points to an apparently non-existent file and yet everything on my local instance looks identical to the Penn State Public site. Thanks, Dan -- next part
[galaxy-dev] Which css file does welcome.html use?
OK, this is ostensibly a simple question. However, I can't find the CSS file that welcome.html is using. In the HTML file, there's this line: link rel=stylesheet href=style/base.css type=text/css / However, I don't see a directory named style anywhere in the galaxy directory tree. When I search for base.css, from the root Galaxy installation directory, I get the following results: ./static/june_2007_style/blue/base.css ./static/light_hatched_style/blue/base.css ./static/light_hatched_style/green/base.css ./static/old_blue_style/base.css So I assume that one of these is being used? I do think it's strange though, that the HTML points to an apparently non-existent file and yet everything on my local instance looks identical to the Penn State Public site. Thanks, Dan ___ 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] How to make trackster jobs run locally instead of on a cluster?
We have an instance of Galaxy deployed on a local institutional cluster. It's working well, but when we import BED files for visualization, Galaxy runs the processing for these on the cluster. I would like to run these tasks locally instead. I understand how to make individual tools run locally, but I'm hoping there's a better way to accomplish what I would like to do without having to specify each of the many conversion tools individually in the universe_wsgi.ini config file. Thanks! Dan ___ 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] Local jobs aren't dispatching in a balanced configuration deployed on a cluster
Good catch, thanks Nate! I have plenty of tool_runners defined, but no tool_handlers. Do I have to specifically assign tool handlers in order for them to be used in job deployment? Thanks! Dan Hi Daniel, This parameter should be 'job_handlers' Are there any entries in your [galaxy:tool_handlers] and/or [galaxy:tool_runners] sections? --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/
[galaxy-dev] Local jobs aren't dispatching in a balanced configuration deployed on a cluster
I have galaxy running on my institution's cluster computing service, which uses PBS. It's in a balanced configuration. Jobs going to the cluster submit without any problem at all. However, any job that I have specified to run locally in the universe_wgsi.ini file won't dispatch. There isn't any record of the job in the manager.log, or any of the handler[#].log files. In fact, I've never seen anything in the handler logfiles after serving on [GALAXY IP]:[SPECIFIC PORT NUMBER OF HANDLER]. The manager logfile has all the details about the jobs dispatched to the pbs runner, but nothing about local jobs. HOWEVER, if I stop Galaxy using GALAXY_RUN_ALL=1 sh ./run.sh --stop-daemon and restart using GALAXY_RUN_ALL=1 sh ./run.sh --daemon then the local jobs that were waiting to run begin immediately. Information about them shows up in manager.log, but not in the handler0.log or handler1.log files. I'm on an 8-core Dell R410 server, if that matters. The server portion of my universe_wsgi.ini file is pasted below. # HTTP Server -- # Configuration of the internal HTTP server. [server:web0] # 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 = localhost # 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 = 7 [server:web1] use = egg:Paste#http port = 8081 host = localhost use_threadpool = true threadpool_workers = 7 [server:manager] use = egg:Paste#http port = 8079 host = localhost use_threadpool = true threadpool_workers = 5 [server:handler0] use = egg:Paste#http port = 8090 host = localhost use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8091 host = localhost use_threadpool = true threadpool_workers = 5 [app:main] # -- Application and filtering job_manager = manager job_handler = handler0,handler1 # Custom Parameters ___ 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] How does Galaxy access datasets?
Thanks Nate! That's very helpful. -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Friday, June 08, 2012 3:31 PM To: Dorset, Daniel C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How does Galaxy access datasets? On Jun 5, 2012, at 6:08 PM, Dorset, Daniel C wrote: I'm trying to troubleshoot why I can't retrieve output from my Galaxy cluster instance. I notice that when I click on any output, the URL is something like: http://[root galaxy address]/datasets/[some 16-character hash]/display/[file name] I'm not able to find the datasets directory on the local machine, and I couldn't figure anything out by searching the paster.log file and the apache access and error logs. Everytime I try to access output, it downloads a zero-byte file. The files that I want to download through Galaxy are in the correct subdirectory of /database/files/... If someone could explain to be what's going on behind the scenes, it would help me quite a bit. I'm guessing that the absolute path is stored in a database, but beyond that I don't know any specifics. If that's the case, knowing the relevant database tables would be a huge hint. Hi Dan, The hash is decoded and converted to an ID using code in lib/galaxy/web/security/__init__.py and the value of id_secret in universe_wsgi.ini. The decoded id is then passed to code in lib/galaxy/objectstore/__init__.py to assemble the path underneath galaxy-dist/database/files/ You may find galaxy-dist/scripts/helper.py in converting history dataset IDs to filesystem paths (they are also available directly in the web interface if you are an administrator or set expose_dataset_path = True in universe_wsgi.ini). --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/
Re: [galaxy-dev] I can't see or access pictures in FastQC
Hi Ross, thanks for the reply! I ran FastQC from the command line, and it did give the proper output. Furthermore, FastQC generating the proper output when I run it from Galaxy. However, Galaxy is having trouble accessing the files. If I go into the filesystem, I can find all of the files in .../database/files/[###]/dataset_[###]_files/ I ran FastQC on the Penn State public instance, and it gives HTML output with pictures in-line and all of the linked files accessible. When I mouseover the link, it looks the same as it does on my local instances, in that the address is in the following format: [Galaxy web address]/datasets/[16 character hash]/display/[filename] Knowing what's going on under the hood would be extremely helpful towards my troubleshooting. So far I can't find anything interesting in paster.log, nor in the Apache log files. Thanks! Dan -Original Message- From: Ross [mailto:ross.laza...@gmail.com] Sent: Wednesday, June 06, 2012 6:07 PM To: Dorset, Daniel C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] I can't see or access pictures in FastQC Hi, Daniel. The wrapper doesn't introduce any new dependencies other than a working FastQC install in the right place so can you please let us know what happens when you run FastQC from the command line as the user running your Galaxy processes - it should start an interactive FastQC session where you can try running a real fastq input and check that you get the HTML outputs. Once it's all working from the command line, try the tool again and let us know how that turns out please? On Thu, Jun 7, 2012 at 6:58 AM, Dorset, Daniel C daniel.dor...@vanderbilt.edu wrote: I'm running two separate instances of Galaxy on two different servers. On both servers, whenever I run FastQC, I can see the result HTML file, but none of the pictures show up. Furthermore, if I try to access the links at the bottom of the page, they don't lead to any real files. If I look in my database/files/subfolder, I see a dataset_### file that contains the HTML info, which I am able to see in Galaxy. There is another folder named dataset_###_files, and all of the pictures and the FastQC results zip file are contained in there. I can access them with full read permissions, and the sizes appear correct. Has anyone else experienced this problem? ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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] I can't see or access pictures in FastQC
I appreciate you taking the time to help! I'm almost positive it's a local configuration issue, like you said, but without knowing how Galaxy generates or parses its internal links (in the form of [Galaxy web address]/datasets/[16 character hash]/display/[filename] ) it's tough to know how to attack the problem. I dug through some of the database tables in psql, but I couldn't find much of interest there either. hg tip result is: 7148:17d57db9a7c0 -- that's the May 9th release Thanks again for your help! Dan ___ 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] How does Galaxy access datasets?
I'm trying to troubleshoot why I can't retrieve output from my Galaxy cluster instance. I notice that when I click on any output, the URL is something like: http://[root galaxy address]/datasets/[some 16-character hash]/display/[file name] I'm not able to find the datasets directory on the local machine, and I couldn't figure anything out by searching the paster.log file and the apache access and error logs. Everytime I try to access output, it downloads a zero-byte file. The files that I want to download through Galaxy are in the correct subdirectory of /database/files/... If someone could explain to be what's going on behind the scenes, it would help me quite a bit. I'm guessing that the absolute path is stored in a database, but beyond that I don't know any specifics. If that's the case, knowing the relevant database tables would be a huge hint. Thanks! Dan ___ 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] Running Galaxy on PBS/Torque cluster
Thanks Nate! I'm looking forward to it! -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Thursday, May 10, 2012 11:02 AM To: Dorset, Daniel C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Running Galaxy on PBS/Torque cluster On May 3, 2012, at 3:42 PM, Dorset, Daniel C wrote: I have had Galaxy running on a local BAS, and after success with that we're ready to create an instance on our local cluster computing service. The local cluster uses PBS/Torque. I'm familiar with the basics of configuration, but our particular scheduler rewards those who specify accurate walltimes. I would like to be able to define specific walltimes for each tool. I'm mapping out a strategy for how best to specify accurate walltimes. For instance, if someone is running tophat, it will take longer if they're mapping against a complex reference genome like human, as opposed to nematode. I'd like to use different walltimes to account for that. Is there anyone who has tackled this and would be willing to share their approach with me? Hi Dan, This doesn't currently exist in Galaxy, but John Chilton at UMN has written enhancements that do what you're looking for: https://bitbucket.org/galaxy/galaxy-central/pull-request/12/dynamic-job-runners Unfortunately the patches no longer apply cleanly against galaxy-central, but I will work on getting them integrated soon. --nate Thanks! Dan ___ 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] FTP Problem: Users cannot see their uploads
Hi Mish, In the proftpd.conf file, do you have the user and group fields set to your Galaxy user and group? Let me know if the question needs further clarification. Thanks, Dan Message: 10 Date: Wed, 9 May 2012 08:21:19 + From: Misharl mon mish...@hotmail.com To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] FTP Problem: Users cannot see their uploads files. Message-ID: dub106-w582aaf4ad01bfb3e1d1069af...@phx.gbl Content-Type: text/plain; charset=iso-8859-1 Hi everybody, I have managed to get proftpd to work, it can connect to the galaxy sql database, and users can log to upload files in their directory. But there is a problem, when a galaxy user logs in the galaxy web platform, the user can't see his upload files since Galaxy doesn't have the rights to open the directory. How can i change the permissions in proftpd so that galaxy can open the user directory? Thanks in advance to all. Mish ___ 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] Running Galaxy on PBS/Torque cluster
I have had Galaxy running on a local BAS, and after success with that we're ready to create an instance on our local cluster computing service. The local cluster uses PBS/Torque. I'm familiar with the basics of configuration, but our particular scheduler rewards those who specify accurate walltimes. I would like to be able to define specific walltimes for each tool. I'm mapping out a strategy for how best to specify accurate walltimes. For instance, if someone is running tophat, it will take longer if they're mapping against a complex reference genome like human, as opposed to nematode. I'd like to use different walltimes to account for that. Is there anyone who has tackled this and would be willing to share their approach with me? Thanks! Dan ___ 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] Interested in speaking with other
Hi Ann, Count me in. Great idea! -Dan ___ 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] How to specify RUM output dir?
Thanks Jeremy, that's very helpful, and it's great to hear from a developer! I have been pursuing option (a), and I feel like I'm very close. The RUM tool runs, and the filesizes show up in the history, but the datasets show up as erroneous. When I click on the apparently-problematic dataset's bug icon, the error message shows the following two lines repeated over 100 times: yes: standard output: Broken pip yes: write error I know what this means, generally, but not in the context of Galaxy. Is this a telltale symptom, or is it too generic to say? Under the additional output, it shows exactly the STDOUT the tool shows when it executes and terminates properly from the command line. So I know I'm close, I feel like I'm missing something small. When I click on the view dataset button, I see the data, and it's legit. When I click Edit Attributes, I see a message at the bottom of the Edit Attributes pane that says Required metadata values are missing. Some of these values may not be editable by the user. Selecting Auto-detect will attempt to fix these values. When I attempt to run the Auto-detect, this notification goes away. It seems like the only issue right now is getting rid of that broken pipe error message. Once that's gone, perhaps the datasets won't be flagged as erroneous and I can use them in downstream processes. If I can get this tool working perfectly, I'll definitely upload it to the Galaxy toolshed. Any tips you could provide would be greatly appreciated! Thanks, Dan You have two options: (a) you can set up the tool to report only a subset of outputs from the tool; or (b) you can use a composite datatype to store the complete directory: http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes Best, J. ___ 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] How to specify RUM output dir?
Fantastic! Knowing that it's not coming from Galaxy is very helpful. Thanks again, Dan -Original Message- From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Thursday, April 19, 2012 1:56 PM To: Dorset, Daniel C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: How to specify RUM output dir? yes: standard output: Broken pip yes: write error I know what this means, generally, but not in the context of Galaxy. Is this a telltale symptom, or is it too generic to say? Hard to say, but it's coming from your script and is indeed causing your job to fail. You might find it easier to debug if you run your tool/wrapper script from the command line. Best, J. ___ 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] How to specify RUM output dir?
I'm currently writing a Galaxy wrapper for RUM (RNA-seq Unified Mapper). RUM is a tool that generates many output files. It is run from the command line using the following syntax: RUM_runner.pl config file reads file(s) output dir num chunks name [options] I'm good with everything except the output dir. I can't figure out how to pass that directory information from Galaxy to the RUM_runner.pl in such a way that Galaxy will be able to subsequently capture the data. Does anybody have any advice, or can someone point me towards an existing wrapper that does something similar? Thanks! Dan ___ 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] Problem capturing output from RUM
I'm writing a wrapper for RUM (RNA-Seq Unified Mapper). For those of you who
aren't familiar with RUM, it produces several output files. I'm trying to
capture 12 of those files in Galaxy.
Here is one of the 12 nodes:
data format=tabular name=feature_quantifications_galaxy
label=${tool.name} on ${on_string}: Feature Quantifications /
All 12 nodes have similar syntax. When I try to run RUM from Galaxy, it's
obvious that the program is executing properly. The outputs show up as pending
until the execution of RUM has completed. However, the output is not being
properly captured. All 12 outputs show up as being in the error state, and when
I click on the bug icon I see the following in the error report:
yes: standard output: Broken pipe
yes: write error
Those two lines are repeated literally over a hundred times. In the additional
output pane beneath the error pane, It shows the output from RUM, which
indicates that the tool indeed ran properly. The text is exactly what I would
expect to see if I ran the tool from the command line without any problems. So
basically, I'm doing something wrong in capturing the output. I have watched
the screencast and perused other wrappers, but I'm not sure at this point where
I'm going wrong. The full text of the wrapper is pasted below:
tool id=rum_all name=RUM version=0.1
!-- Run all steps of RUM (RNA-seq Unified Mapper). Mapper written by Dan
Dorset at Vanderbilt GSR. Email with questions: daniel.dor...@vanderbilt.edu
Wrapper status is alpha --
description: RNA-Seq Unified Mapping/description
requirements
requirement type=packagerum/requirement
/requirements
command
##IMPORTANT!!! You will need to change this to correspond to the
specific installation path of RUM on your server
perl /data/dorsetdc/rum/bin/RUM_runner.pl
##Reference Genome
##IMPORTANT!!! You will need to change this to correspond to the
specific installation path of RUM on your server
/data/dorsetdc/rum/conf/rum.config_$refgenome
## Inputs.
#if $inputs.paired_or_single == paired:
$inputs.left_input,,,$inputs.right_input
#else:
$inputs.input
#end if
##output directory
./
## Number of CPU cores
##IMPORTANT!!! Make sure you set the max value to something
appropriate for your system. See the RUM tool manpage for more details
#if $additional_params.use_additional == yes:
$additional_params.num_cores
#else:
16
#end if
##data name (static for now)
galaxy
## Additional parameters.
#if $additional_params.use_additional == yes:
-min_contig_length $additional_params.min_contig_length
#if $additional_params.strandspecific == yes
-strand_specific
#end if
#if $additional_params.dnamode == yes
-dnamode
#end if
#if $additional_params.count_mismatches == yes
-countmatches
#end if
#end if
/command
inputs
conditional name=inputs
param name=paired_or_single type=select label=Paired or
Single-end data?
option value=pairedPaired/option
option value=singleSingle/option
/param
when value=paired
param format=fasta,fastq name=left_input type=data
label=Left/Forward strand reads help=/
param format=fasta,fastq name=right_input type=data
label=Right/Reverse strand reads help=/
/when
when value=single
param format=fasta,fastq name=input type=data
label=Single-end reads help=/
/when
/conditional
param name=refgenome type=select label=Select Reference
Genome
option value=hg19Human (hg19)/option
option value=mm9Mouse (mm9)/option
/param
conditional name=additional_params
param name=use_additional type=select label=Use Additional
Params?
option value=noNo/option
option value=yesYes/option
/param
when value=no
/when
when value=yes
param name=min_contig_length type=integer value=200
min=1 label=Minimum Contig Length help=/
param name=num_cores type=integer
value=16 min=1 max=32 label=Number of Cores to Use help=Min of 1, max
of 32 /
param name=strandspecific type=select
label=Are the Data Strand Specific?
option value=noNo/option
Re: [galaxy-dev] Error while uploading
Hi Luciano, I had a similar problem with our local instance of Galaxy. In our case, the /tmp directory was filling up, causing the job to abort. We had Galaxy running on a partition with tons of disk space, but the partition on which /tmp was located had substantially less free disk space. Try running the df command from the Linux command line. If you don't know how to interpret its output, let me know. Certain tasks that run on behalf of Galaxy, like gzip for decompressing large datasets, will store intermediate temporary data in /tmp instead of a subdirectory within your Galaxy installation. Let me know if that solves your issue, Dan Message: 1 Date: Sat, 10 Mar 2012 17:25:38 -0600 From: Luciano Cosme cosme.sim...@gmail.com To: Galaxy-dev galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Error while uploading Message-ID: camasfsjdm0udcivqk7p-mpijr8ualxe0zx7szug4upsqj_n...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I uploaded 11 files today (1 to 2Gb compressed files) to my local instance without a problem (as admin). Then I got this error message below and it get stuck at This dataset is uploading and I could not upload the last files. Is there anything I can do to solve it? What I notice is that I can still upload small files, before I concatenate them. I have 15 time points and some of them have up to 20 files, so it is easier to concatenate them and them upload. Thank you. Luciano ___ 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/
