[galaxy-user] Illumina Methylation tool in toolshed
Hi, This is my third post regarding this matter but however I didn't get any reply. I am trying to find a tool for r Illumina Methylation. Is there any available on the tool shed or test tool shed? 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/
Re: [galaxy-user] Illumina Methylation tool in toolshed
Hi Bjoern, Thank you for your reply. To be precise I am looking for a wrapper of * lumi. *http://www.bioconductor.org/packages/2.12/bioc/html/lumi.html Do we have that in main tool shed or test tool shed or in github? Thanks, Sachit On Mon, Jul 29, 2013 at 2:53 PM, Bjoern Gruening bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Sachit, not in the toolshed but you can find a start here: https://github.com/bgruening/galaxytools/tree/master/illumina_methylation_analyser its for the 450k chips, I have also some tools for WGMA if you are interested. Cheers, Bjoern Hi, This is my third post regarding this matter but however I didn't get any reply. I am trying to find a tool for r Illumina Methylation. Is there any available on the tool shed or test tool shed? 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/
Re: [galaxy-user] Rename tool output file in Galaxy
Hi, By i do you mean Edit attributes button? There are four sub-headings on that: Attributes, Convert format, Datatype and permissions but I can't see data file's full path on any of them. What's wrong? On Wed, Jul 24, 2013 at 3:05 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, Jul 24, 2013 at 5:21 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: 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. Via the i icon of a history entry (information) you can see the datafile's full path which includes the ID. 2) Can I rename my output while initiating the task? If I can how can I do this and what are the consequences. Yes, you can. Normally this is fine. (Note sure if there can be complications with meta-data normally added automatically by inspecting the finished file...) Peter ___ 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/
Re: [galaxy-user] Rename tool output file in Galaxy
Yes, but unfortunately that didn't work too. I have already tried the solution you provided. I could edit the tags and annotations but it won't change the file name in my file system. The file is still named as * dataset_43649.dat. * On Wed, Jul 24, 2013 at 3:52 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, Jul 24, 2013 at 10:35 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: Hi, By i do you mean Edit attributes button? There are four sub-headings on that: Attributes, Convert format, Datatype and permissions but I can't see data file's full path on any of them. What's wrong? No, not the edit button. First click on a dataset's title so it expands. You should see a snippet of data etc plus a row of icons (save, information, reload in bottom left of the history, and tags and annotation bottom right). Peter ___ 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/
Re: [galaxy-user] Rename tool output file in Galaxy
Thanks Peter for clearing this out. On Wed, Jul 24, 2013 at 4:33 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, Jul 24, 2013 at 11:15 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: Yes, but unfortunately that didn't work too. I have already tried the solution you provided. I could edit the tags and annotations but it won't change the file name in my file system. The file is still named as dataset_43649.dat. You *cannot* rename the file on disk (without bypassing Galaxy and editing the database and renaming the file directly). This is by design - unless you are an administrator debugging something or a tool author you don't need to know the actual filename on disk. You *can* rename the description of the file as shown within the Galaxy interface (via edit attributes). Peter ___ 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/
[galaxy-user] Rename tool output file 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 ___ 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/
[galaxy-user] Rename tool output file 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 ___ 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/
Re: [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/ ___ 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/
[galaxy-user] Regarding galaxy wrappers: lumi, DESeq edgeR
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/
[galaxy-user] 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 ___ 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/
Re: [galaxy-user] 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 ___ 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/
[galaxy-user] Error in TopHat
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 ___ 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/
Re: [galaxy-user] 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 ___ 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/
[galaxy-user] 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? ___ 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/
[galaxy-user] 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 ___ 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/
[galaxy-user] How to add a built-in index for Tophat2?
TopHat2 needs built-in index/ reference genome in order for it to run. I need to add hg 16 index into the build-in index / reference gnome list. I already have the file. How can I add it? Regards, 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/
[galaxy-user] Problem in Manage data Library
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? Regards, 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/
[galaxy-user] Bismark Error: Data table named 'bismark_bs_indeces' is required by tool but not configured.
Hi all, I am seeing this error while clicking on Bismark in Galaxy. I got the Bismark for galaxy tool shed. I tried to get another bismark wrapper developed by Bjoern. I didnt know how to download that. What's the error? Thanks ___ 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/
[galaxy-user] User's information
Where are the user's information stored in Galaxy? I can't find the information in universe_wsgi. Regards, 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/
[galaxy-user] Getting error in Bismark
I am getting this error at the top while opening Bismark Mapper: Data table named 'bismark_bs_indeces' is required by tool but not configured. I got Bismark from official toolshed. ___ 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/
[galaxy-user] Data table named 'bowtie2_indexes' is required by tool but not configured
I am getting this error in Bowtie2 and Tophat2: Data table named 'bowtie2_indexes' is required by tool but not configured Data table named 'tophat2_indexes' is required by tool but not configured. How can I solve it? Thanks ___ 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/
Re: [galaxy-user] Data table named 'bowtie2_indexes' is required by tool but not configured
Thanks but after adding those lines when I stop and started the server using --daemon mode, the server is not working? What might be the problem? On Fri, Oct 19, 2012 at 9:01 AM, Jeremy Goecks jeremy.goe...@emory.eduwrote: You'll need to update the tool_data_table_conf.xml file in your Galaxy home directory. If you haven't made changes to the file, you can copy tool_data_table_conf.xml.sample to tool_data_table_conf.xml If you have made changes, add these entries to the file: -- table name=bowtie2_indexes comment_char=# columnsvalue, dbkey, name, path/columns file path=tool-data/bowtie2_indices.loc / /table table name=tophat2_indexes comment_char=# columnsvalue, dbkey, name, path/columns file path=tool-data/bowtie2_indices.loc / /table -- Finally, please direct questions about local Galaxy installations to the galaxy-dev mailing list: galaxy-...@bx.psu.edu Best, J. On Oct 19, 2012, at 2:58 AM, Sachit Adhikari wrote: I am getting this error in Bowtie2 and Tophat2: Data table named 'bowtie2_indexes' is required by tool but not configured Data table named 'tophat2_indexes' is required by tool but not configured. How can I solve it? Thanks ___ 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/ ___ 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/
[galaxy-user] Can't seem to stop or restart the Galaxy in server
Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___ 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/
Re: [galaxy-user] Can't seem to stop or restart the Galaxy in server
Thanks. Helped me! On Thu, Oct 18, 2012 at 11:02 AM, Enis Afgan eaf...@emory.edu wrote: With a certain version of Python there's been an issue stopping Galaxy using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in the background and then 'sh run.sh --stop-damemon' to stop it. Hope this helps, Enis On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari sachit.techner...@gmail.com wrote: Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___ 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/ ___ 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/
[galaxy-user] Are tools must be installed in local machine?
Hello. The tools like Tophat, Bowtie etc are pre-installed in Galaxy. Are those tools must be installed in order to work in Galaxy. For example: I am using Debian machine(Don't have tophat and bowtie installed). Will tophat and bowtie work in my local galaxy? Thanks ___ 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/
Re: [galaxy-user] Are tools must be installed in local machine?
I don't think you understood my question very well. Tophat and Bowtie are available by default in Galaxy. Tophat and Bowtie however is not installed in my operating system. Will it still work in Galaxy? On Mon, Oct 8, 2012 at 3:22 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Sachit, you need to install such tools by yourself, unless you are using some new tools from the toolshed. For example the ncbi-tools or BWA from the toolshed are capable of installing all dependency automatically. In the future the plan is to move all heavy tools to the toolshed with automatic dependency and version handling, afaik. Regards, Bjoern Hello. The tools like Tophat, Bowtie etc are pre-installed in Galaxy. Are those tools must be installed in order to work in Galaxy. For example: I am using Debian machine(Don't have tophat and bowtie installed). Will tophat and bowtie work in my local galaxy? Thanks ___ 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/ ___ 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/
Re: [galaxy-user] RSEM on Galaxy
Hi there Alicia! To find the tool in the Galaxy tool search, first you have to put your tool files in tools with .xml files then you have to edit tool_conf.xml file. Here's the step by step tutorial: http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial Regards, Sachit On Fri, Oct 5, 2012 at 8:55 PM, Victor ruo...@wisc.edu wrote: Hi Alicia, At the moment you have to install the wrapper manually. That is, the current version of the RSEM won't automatically install the rsem binaries for you. We are working on updating the tool from the tool shed. The readme file within the tarball provides instructions on what version of RSEM to install and other details. We ll keep you posted as soon as we update the tool so things will be done for you much like the other newer tools in the tool shed. Thank you for using RSEM and please let me know how it goes. Victor On Oct 5, 2012, at 7:14 PM, Ross ross.laza...@gmail.com wrote: Alicia, Some relevant details usually make it easier for list members to help you - please see http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions Did you load the offending tool from a toolshed or is it a tool wrapper you wrote yourself? If the latter, I have two suggestions: 1) Search paster.log for your tool name and make sure it got correctly loaded when you restarted Galaxy - xml syntax errors like misplaced characters will break the tool loading process. 2) if the log shows that it loaded, make sure you refresh the tool frame in your browser after restarting Galaxy - eg clicking the analyse data tab will get rid of the old cached copy. On Sat, Oct 6, 2012 at 10:02 AM, Alicia R. Pérez-Porro alicia.r.perezpo...@gmail.com wrote: Hi all, Recently i installed RSEM into Galaxy. The problem is that now i cannot find the tool when i open my galaxy in my computer. I checked and rsem folder is inside the tool folder. Any suggestions? Thanks, Alicia. -- Alicia R. Pérez-Porro PhD student Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/ Department of Marine Ecology Center for Advanced Studies of Blanes (CEAB-CSIC) C/Accés Cala St. Francesc 14 17300 Blanes, Girona, SPAIN phone: +34 972 336 101 fax: +34 972 337 806 www.ceab.csic.es ___ 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/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ 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/ ___ 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/ ___ 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/
[galaxy-user] Trim Galore Galaxy Integration
Hello. I would like to integrate this great tool Trim Galore in the local Galaxy. Has anyone did this before? If so, please provide me with the wrapper and .xml file? How can I integrate it? Best wishes, 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/
[galaxy-user] Trim Galore Galaxy Integration
Hello. I would like to integrate this great tool Trim Galore in the local Galaxy. How can I do that? Thanks in advance. ___ 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/
