May 2012 - galaxy-dev - lists.galaxyproject.org

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09 May '12

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R scripts for DESeq
by Jennifer Jackson 09 May '12

09 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 Tool Shed upload error
by Vipin TS 09 May '12

09 May '12

Hi Galaxy team, I am trying to upload a tool wrapper to main tool shed http://toolshed.g2.bx.psu.edu and ending up with a 'server error' message. Could you please let me know what is going wrong here. thanks, --Vipin

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Server Error when downloading files from history
by Rathi D. Thiagarajan 09 May '12

09 May '12

Hi there, I received the following error when trying to download/save my tabular files with 5k lines: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Please help! Thanks in advance. Cheers, Rathi -- Rathi D. Thiagarajan, PhD Professional Scientific Collaborator UCSD Research Scholar Dept. of Chemical Physiology Center for Regenerative Medicine The Scripps Research Institute 3030 Science Park Rd, La Jolla, CA 92035, USA Mail:SP30-3021 W: 858.784.7753 E: rathi(a)scripps.edu E: rthiagarajan(a)ucsd.edu

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problems with running jobs on Galaxy
by Philipp Kapranov 09 May '12

09 May '12

Hello, I keep on getting this error today: Error executing tool: [Errno 13] Permission denied: '/galaxy/main_pool/pool4/files/004' . What is wrong? Thank you! Phil

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server error
by Ashley Tehranchi 09 May '12

09 May '12

Hi, I have run into a server error, how can I fix it? Thanks, Ashley

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bowtie -X
by Xu, Jianpeng 09 May '12

09 May '12

Hi, I noticed that there is a parameter: Maximum insert size for valid paired-end alignments (-X) for bowtie on Galaxy. The default value on Galaxy is -X 1000. I was wondering if this is the default value we should use ? Or we need to change it to another value ? Thanks a lot. Jianpeng ________________________________ 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).

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Problem downloading results from MACS
by Yanina Bogliotti 09 May '12

09 May '12

Hi, I'm using Galaxy from the cloud (ID: pross(a)ucdavis.edu) and I'm trying to download some .xls files (MACS' results that were successfully finished) and I'm obtaining the following error message: *Server Error** An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)* Please let me know how can I solve this problem. Thanks a lot, Yanina

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Re: [galaxy-dev] FTP Problem: Users cannot see their uploads
by Dorset, Daniel C 09 May '12

09 May '12

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 +0000 From: Misharl mon <misharl(a)hotmail.com> To: <galaxy-dev(a)lists.bx.psu.edu> Subject: [galaxy-dev] FTP Problem: Users cannot see their uploads files. Message-ID: <DUB106-W582AAF4AD01BFB3E1D1069AF110(a)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

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Sub-task splitting
by Peter Cock 09 May '12

09 May '12

Hello all, Currently the Galaxy experimental task splitting code allows splitting into N chunks, e.g. 8 parts, with: <parallelism method="multi" split_mode="number_of_parts" split_size="8" ..." /> Or, into chunks of at most size N (units dependent on the file type, e.g. lines in a tabular file or number of sequences in FASTA/FASTQ), e.g. at most 1000 sequences: <parallelism method="multi" split_mode="to_size" split_size="1000" ... /> As an aside I found it confusing that the meaning of the "split_size" attribute depend on the "split_mode" (number of jobs, or size of jobs). I would prefer to be able to set both sizes - in this case tell Galaxy to try to use at least 8 parts, each of at most 1000 sequences. Thus in a BLAST task, initially the split would be (up to) eight ways: 8 queries => 8 jobs each with 1 query 80 queries => 8 jobs each with 10 queries 800 queries => 8 jobs each with 100 queries 8000 queries => 8 jobs each with 1000 queries Then, once the max chunk size comes into play, you'd just get more jobs: 9000 queries => 9 jobs each with 1000 queries 10000 queries => 10 jobs each with 1000 queries 20000 queries => 20 jobs each with 1000 queries etc The appeal of this is it takes advantage of parallelism for small jobs (under 100 queries) and large jobs (1000s of queries), while able to impose a maximum size on each cluster job. The problem is this requires changing the XML tags, and getting rid of the current two modes in favour of this combined one. Perhaps this: <parallelism method="multi" min_jobs="8" max_size="1000" ... /> The jobs threshold isn't strictly a minimum - if you have N < 8 query sequences, you'd just have N jobs of 1 query each. Does this sound sufficiently general? The split code is still rather experimental so I don't expect breaking the API to be a big issue (not many people are using it). Peter

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