[galaxy-dev] Lumi wrapper for Galaxy
Hello group, I am trying to write lumi wrapper for Galaxy. Is anyone is writing or already have written lumi wrapper for Galaxy. I couldn't find in both galaxy main tool shed and test tool shed. Regards Sachit ___ 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] Invitation to connect on LinkedIn
LinkedIn galaxy-...@bx.psu.ed, I'd like to add you to my professional network on LinkedIn. - sachit sachit adhikari Software Engineer at ZurelSoft Nepal Nepal Confirm that you know sachit adhikari: https://www.linkedin.com/e/1kvf56-hjf9os56-3g/isd/15160415460/FH4R02On/?hs=falsetok=0gQT6_MazFyRQ1 -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/1kvf56-hjf9os56-3g/qaQIbd-APagZF22GBAQuFmcZcI_00a44mJ/goo/galaxy-dev%40bx%2Epsu%2Eedu/20061/I5047310806_1/?hs=falsetok=2tRUJSiarFyRQ1 (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. ___ 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] Rename output while initiating the task in galaxy
Hi group, The galaxy stores the output of the job on files/043/dataset_*ID*.dat. I have two questions here.: 1) Can I find the ID of my output from the Galaxy history? I tried Edit Attributes, Annotations, tags but couldn't find it. 2) Can I rename my output while initiating the task? If I can how can I do this and what are the consequences. Thank you. Regards, Sachit ___ 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] Regarding galaxy wrappers: lumi, DESeq edgeR
Sorry about that Ross. I would try your wrapper of edgeR and would happily report you the bug. Can you make me the link of Galaxy Test Toolshed? Thanks, Sachit On Mon, Jul 8, 2013 at 11:51 AM, Ross ross.laza...@gmail.com wrote: (Sachit, please don't cross-post to the dev and user lists?) There's a beta version of an edgeR/deseq/voom wrapper and a companion htseq based count matrix maker in the test toolshed statistics section owned by me - fubar. Definitely not quite ready for production but installable and I'd appreciate feedback from anyone brave enough to try them out. Best installed on a test instance you plan on destroying because the R 3.0 dependency is about to swap over to Bjorns better one - should be done later this week when I get some time. Be warned it takes a long time to auto-install - 10-15 minutes or so on my laptop. On Mon, Jul 8, 2013 at 3:36 PM, Sachit Adhikari sachit.techner...@gmail.com wrote: Hi, These are the R libraries. Have anyone written a wrapper for these libraries lumi, DESeq edgeR? Thanks, Sachit ___ 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/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ 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] [galaxy-user] Regarding galaxy wrappers: lumi, DESeq edgeR
Thank you Björn and Ross. I will install the tools from the admin interface. On Mon, Jul 8, 2013 at 12:35 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Sachit, we are working currently on a DESeq2 wrapper. Not yet finised sorry. There is also a edgeR Test repository from Ross Lazarus under: http://testtoolshed.g2.bx.psu.edu/view/fubar/edger_test Work is in progress, help is welcome! Ciao, Bjoenr Hi, These are the R libraries. Have anyone written a wrapper for these libraries lumi, DESeq edgeR? Thanks, Sachit ___ 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/ 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] Problem uploading file !!
Galaxy recommends to upload the file more than 2 GB via FTP. Browser can't handle the large file upload. Thank you! On Sat, Apr 20, 2013 at 3:07 AM, Nishant THAKUR tha...@ciml.univ-mrs.frwrote: Hello, I installed galaxy server on ubuntu recently, I can upload small fastq files (~600 Mb), but when I am uploading large file(2.7 gb), it is taking forever. Could you please suggest me something ? Best regards Nishant Thakur ___ 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] How to be an admin?
Hi, First make sure that the you are editing the correct universe_wsgi.ini file. Secondly, you must restart your server after you make changes to your settings file i.e universe_wsgi.ini. If you are running your server in daemon mode use following command to stop your server: *sh run.sh --stop-daemon* Then again start your server using the following command in a daemon mode: *sh run.sh --daemon* * * On Wed, Apr 10, 2013 at 3:38 AM, Marc Logghe marc.log...@ablynx.com wrote: Hi Tobias, Maybe your Galaxy is running in daemon mode. If that is the case, if you do 'ps aux | grep universe' you will see something like: python ./scripts/paster.py serve universe_wsgi.ini --daemon You should first stop the daemon. Or you kill it, or you type in the galaxy home './run.sh stop'. Check again via ps to assure yourself the daemon has stopped. Now, start galaxy again. HTH, Marc -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Tobias Hohenaur Sent: Tuesday, April 09, 2013 3:59 PM To: Dannon Baker Cc: Galaxy Dev Subject: Re: [galaxy-dev] How to be an admin? Thank you for hinting the reload option. I opened the universe_wsgi.ini in the galaxy-dist folder and changed the port to 8081, the host to 0.0.0.0, then saved. The server reloads, but the changes have not taken effect. It is still at 127.0.0.1 and 8080... As far as I can see there is no other universe_wsgi.ini file except one that is calles universe_wsgi.ini sample. - Original Message - From: Dannon Baker dannon.ba...@gmail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: Peter Cock p.j.a.c...@googlemail.com,Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 2013-04-09 22:47:04 Subject: Re: [galaxy-dev] How to be an admin? Yeah, if you're running it with just `run.sh`, that should work fine. One thing you can do if you're going to be tweaking a bunch of settings would be to run it with the reload option enabled `run.sh --reload`. When you change the port in universe_wsgi.ini in the galaxy directory, kill the server and restart, in the log at the end you should see something like: serving on 0.0.0.0:new port view at http://127.0.0.1:new port If you're not seeing that, I'd verify that you're editing the correct universe_wsgi.ini. Perhaps you have multiple galaxies installed somehow? On Tue, Apr 9, 2013 at 9:39 AM, Tobias Hohenaur hohena...@brain.riken.jpwrote: I just hit ctrl c in the terminal to stop. Is that enough? - Original Message - From: Dannon Baker dannon.ba...@gmail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: Peter Cock p.j.a.c...@googlemail.com,Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 2013-04-09 22:30:38 Subject: Re: [galaxy-dev] How to be an admin? How is it that you're restarting the server? It might be useful to check galaxy's log to see what's going on -- this would be paster.log in your galaxy directory or perhaps the foreground of the terminal you're executing galaxy from. -Dannon On Tue, Apr 9, 2013 at 9:25 AM, Tobias Hohenaur hohena...@brain.riken.jpwrote: That does not help. Actually, I tried to change random things in the universe_wsgi.ini, like setting the port to 8081, but none of the changes take effect when I restart the server. I am confused... - Original Message - From: Peter Cock p.j.a.c...@googlemail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: galaxy-dev@lists.bx.psu.edu Date: 2013-04-07 23:28:31 Subject: Re: [galaxy-dev] How to be an admin? On Sun, Apr 7, 2013 at 1:27 PM, Tobias Hohenaur hohena...@brain.riken.jp wrote: Hello, I just installed and updated a local instance of Galaxy on my mac. I then created a user and set the according username (email) as admin in the universe_wsgi.ini file. When I save and restart the server no admin panel appears. What am I doing wrong? Thank you very much for your help! Tobias Make sure you are logged in, and that the email address of your Galaxy account matches the universe_wsgi.ini setting exactly (case may be important). Also the setting used to have problems with extra white space (but I think that was fixed). 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
[galaxy-dev] Error while writing data in tophat2
Galaxy is working fine in command line whereas in Galaxy at last i got this error: [2013-02-15 01:39:12] Reporting output tracks [FAILED] Error running /usr/local/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 50 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 2 --min-segment-intron 50 --max-segment-intron 50 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam Loading ...done Is it a known bug? ___ 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] Fwd: Error while writing data in tophat2
-- Forwarded message -- From: Sachit Adhikari sachit.techner...@gmail.com Date: Fri, Feb 15, 2013 at 11:02 AM Subject: Error while writing data in tophat2 To: galaxy-dev@lists.bx.psu.edu Galaxy is working fine in command line whereas in Galaxy at last i got this error: [2013-02-15 01:39:12] Reporting output tracks [FAILED] Error running /usr/local/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 50 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 2 --min-segment-intron 50 --max-segment-intron 50 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam Loading ...done Is it a known bug? ___ 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 redirect output of all the galaxy tools to another directory?
I want to redirect the output. For example the output of tophat2 is stored in ./tophat2 I want to redirect it to my location. On Thu, Feb 14, 2013 at 7:32 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: you can change the location where all the dataset files are stored in universe_wsgi.ini: # Dataset files are stored in this directory. file_path = database/files if this is, what you want? Regards, Hans-Rudolf On 02/14/2013 05:40 AM, Sachit Adhikari wrote: I want to redirect all the output of Galaxy to another directory(actually a external hard drive with full write access). How can I do that? Thanks __**_ 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] hg19 reference gnome for Tophat2
I tried with many data but still the same problem and regarding settings I haven't changed a thing of Tophat2. What might be causing this error? Thanks On Wed, Feb 13, 2013 at 7:10 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: If the other outputs are fine, then the problem is likely with your data and/or your Tophat settings. Good luck, J. On Feb 13, 2013, at 8:22 AM, Sachit Adhikari wrote: Ok sorry. I did that, but the output of splice junctions is empty. The other outputs looks fine. What might be the problem? Thanks, Sachit On Wed, Feb 13, 2013 at 1:20 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: Shall I replace: /orig/path/hg19hg19hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Yes, that's correct. Finally, please email only galaxy-dev with questions about local installations; galaxy-user is for questions about how to use Galaxy. 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] Error executing tophat2
I got this error which executing tophat2 in Galaxy: Error in tophat: [2013-02-13 02:02:43] Beginning TopHat run (v2.0.7) --- [2013-02-13 02:02:43] Checking for Bowtie Bowtie version:2.0.6.0 [2013-02-13 02:02:43] Checking for Samtools Samtools version:0.1.18.0 [2013-02-13 02:02:43] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/.*.bt2) The tool produced the following additional output: TopHat v2.0.7 tophat2 -p 4 /data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/ /opt/galaxyprod/galaxy-dist/database/files/000/dataset_197.dat I have these files under the Index directory: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.fa genome.rev.1.bt2 genome.rev.2.bt2 tophat_out ___ 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] hg19 reference gnome for Tophat2
Ok sorry. I did that, but the output of splice junctions is empty. The other outputs looks fine. What might be the problem? Thanks, Sachit On Wed, Feb 13, 2013 at 1:20 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: Shall I replace: /orig/path/hg19hg19hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Yes, that's correct. Finally, please email only galaxy-dev with questions about local installations; galaxy-user is for questions about how to use Galaxy. 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] Error executing tophat2
Thanks, that's what I was missing. On Wed, Feb 13, 2013 at 7:09 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: Error in tophat: [2013-02-13 02:02:43] Beginning TopHat run (v2.0.7) --- [2013-02-13 02:02:43] Checking for Bowtie Bowtie version:2.0.6.0 [2013-02-13 02:02:43] Checking for Samtools Samtools version:0.1.18.0 [2013-02-13 02:02:43] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/.*.bt2) The tool produced the following additional output: TopHat v2.0.7 tophat2 -p 4 /data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/ /opt/galaxyprod/galaxy-dist/database/files/000/dataset_197.dat I have these files under the Index directory: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.fa genome.rev.1.bt2 genome.rev.2.bt2 tophat_out Your path to your indices should like like this: /data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/ *genome* * * 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 redirect output of all the galaxy tools to another directory?
I want to redirect all the output of Galaxy to another directory(actually a external hard drive with full write access). How can I do that? Thanks ___ 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] Incomplete tophat2 output
Tophat2 output on accepted hits, deletions and insertions is fine whereas splice junctions output is only: track name=junctions description=TopHat junctions I am running tophat2 with hg19 reference genome? What might be the 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/
[galaxy-dev] hg19 reference gnome for Tophat2
I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index with the files: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.rev.1.bt2 genome.rev.2.bt2 While adding the reference gnome, I need to edit bowtie2_indices.loc Shall I replace: /orig/path/hg19hg19hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Thanks, Sachit ___ 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] hg19 reference gnome for Tophat2
Also, do I have make all the reference files executable? On Wed, Feb 13, 2013 at 6:39 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index with the files: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.rev.1.bt2 genome.rev.2.bt2 While adding the reference gnome, I need to edit bowtie2_indices.loc Shall I replace: /orig/path/hg19hg19hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Thanks, Sachit ___ 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] What is the difference between the table stored_workflow and workflow in Galaxy?
Greetings all, These are various tables related to workflow in Galaxy that I found in the database. There are very similar tables like: workflow and stored_workflow, workflow_step_tag_association, stored_workflow_tag_association etc. I want to know what does specific table holds. What are the fundamental differences between workflow and stored_workflow? Is there Galaxy documentation available for it? If so, please provide me the link. Cheers, Sachit ___ 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] Where is the workflow stored in Galaxy?
Thanks Dannon for the help. Appreciate it. On Fri, Dec 28, 2012 at 8:37 AM, Dannon Baker dannonba...@me.com wrote: Yes, there is a relationship - in the database there's also a WorkflowStepConnection table that relates inputs and outputs (WorkflowStep + i/o name) between steps. On Dec 28, 2012, at 8:33 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: Hi Dannon, Thank you for your answer. What I meant by the last question is that: When I create a workflow (tophat-bowtie-bowtie2). The input is first processed by tophat and the output of tophat is processed by bowtie and then the output of bowtie and processed by bowtie2 and that's the final output. There's some sort of relationship, right? Is this relationship stored in database? On Fri, Dec 28, 2012 at 7:34 AM, Dannon Baker dannonba...@me.com wrote: A workflow is just the definition of a particular process or set of steps. This information is stored in the database (see Workflow, StoredWorkflow, WorkflowStep tables). Running that workflow creates datasets in a history (datasets which are stored in database/files). And, I'm not sure exactly what you're asking in your last question, can you clarify? -Dannon On Dec 28, 2012, at 2:16 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: I have searched the mailing list and found that the output, histories and workflows are stored in ~/database/files. To do a little experiment I deleted all the inside that directory. I then open my Galaxy and browse the workflow. But the workflow is still there. I was wondering where is the workflow stored in Galaxy? Also, if possible can I know how is the relationship specified by user while creating workflow is stored? Happy New year Regards, Sachit ___ 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] Where is the workflow stored in Galaxy?
I have searched the mailing list and found that the output, histories and workflows are stored in ~/database/files. To do a little experiment I deleted all the inside that directory. I then open my Galaxy and browse the workflow. But the workflow is still there. I was wondering where is the workflow stored in Galaxy? Also, if possible can I know how is the relationship specified by user while creating workflow is stored? *Happy New year* Regards, Sachit ___ 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] Where is the output of tools stored in Galaxy?
Hello Everyone, *Merry Christmas and Happy New Year* * * I was wondering where are the output of the tools stored in the machine where the galaxy is hosted? And, can I change the path of the output of the tools? Thanks, Sachit ___ 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 in TopHat
And when I tried running tophat alone like this: tophat -r 20 test_ref reads_1.fq reads_2.fq I get this error: [2012-12-19 06:57:07] Beginning TopHat run (v2.0.7) --- [2012-12-19 06:57:07] Checking for Bowtie Bowtie version: 2.0.2.0 [2012-12-19 06:57:07] Checking for Samtools Samtools version: 0.1.18.0 [2012-12-19 06:57:07] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (test_ref.*.bt On Wed, Dec 19, 2012 at 10:38 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: This is the error I am getting while running Tophat. What's causing this? I have the default hg19 index files. Error in tophat: [Tue Dec 18 10:08:33 2012] Beginning TopHat run (v1.3.3) --- [Tue Dec 18 10:08:33 2012] Preparing output location ./tophat_out/ [Tue Dec 18 10:08:33 2012] Checking for Bowtie index files Error: Could not find Bowtie index files /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19.* TopHat v1.3.3 TopHat v1.3.3 tophat -p 4 /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19 /opt/galaxyprod/galaxy-dist/database/files/000/dataset_45.dat ___ 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] Urgent: Seems like tophat2 does not support --transcriptome-mismatches
It seems like tophat2 does not support --transcriptome-mismatches option but Galaxy is still configured to call tophat2 with this option when run with Full parameter setting option within Galaxy. Is there new wrapper with this fix? If not, how to remove this option from Galaxy so that tophat2 is not call with this option. I am assuming that this is specified somewhere in the wrapper. Thanks, Sachit ___ 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 add to add hg16 index into the build-in index / reference gnome list?
How do I add hg16 into the build-in index? ___ 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] Doesn't have enable_beta_job_managers options in configuration file
My Galaxy Doesn't have enable_beta_job_managers option in universe_conf.ini file. ___ 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] Galaxy doesn't detect the file when we add dataset to a library under Manage data libraries
Hi list, We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select Copy file into Galaxy under Copy data into Galaxy? option and does not detect it when we select Link to files ... Is this a known issue? If it is, is there any workaround to solve the issue? Thanks Regards, Sachit ___ 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] Galaxy doesn't detect the file when we add dataset to a library under Manage data libraries
Hello Everyone, We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select Copy file into Galaxy under Copy data into Galaxy? option and does not detect it when we select Link to files ... Is this a known issue? If it is, is there any workaround to solve the issue? Thanks Regards, Sachit ___ 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] (no subject)
Hello Everyone, I am about to write a syncing tool for Galaxy like Dropbox using Python with the progress bar. How do I integrate it with galaxy? It would be easy for client to upload files using the syncing tool. Are there any syncing tools available for Galaxy? Thanks ___ 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/
