[galaxy-user] Trim Galore Galaxy Integration

2012-10-04 Thread Sachit Adhikari
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

[galaxy-user] Trim Galore Galaxy Integration

2012-10-04 Thread Sachit Adhikari
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

Re: [galaxy-user] RSEM on Galaxy

2012-10-05 Thread Sachit Adhikari
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

[galaxy-user] Are tools must be installed in local machine?

2012-10-08 Thread Sachit Adhikari
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

Re: [galaxy-user] Are tools must be installed in local machine?

2012-10-08 Thread Sachit Adhikari
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

[galaxy-user] Can't seem to stop or restart the Galaxy in server

2012-10-17 Thread Sachit Adhikari
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

Re: [galaxy-user] Can't seem to stop or restart the Galaxy in server

2012-10-17 Thread Sachit Adhikari
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

[galaxy-user] Bowtie2 and Tophat2 for Galaxy

2012-10-18 Thread Sachit Adhikari
Hello Everyone, Can someone please give me the link to download .py file and the wrapper(.xml) of Bowtie2 and Tophat2? Thanks ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public

[galaxy-user] Data table named 'bowtie2_indexes' is required by tool but not configured

2012-10-19 Thread Sachit Adhikari
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

Re: [galaxy-user] Data table named 'bowtie2_indexes' is required by tool but not configured

2012-10-19 Thread Sachit Adhikari
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

[galaxy-user] Using syncing tool in Galaxy

2012-10-31 Thread Sachit Adhikari
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

[galaxy-user] Getting error in Bismark

2012-11-01 Thread Sachit Adhikari
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

[galaxy-user] Bismark Error: Data table named 'bismark_bs_indeces' is required by tool but not configured.

2012-11-29 Thread Sachit Adhikari
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

[galaxy-user] User's information

2012-11-29 Thread Sachit Adhikari
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

[galaxy-user] Problem in Manage data Library

2012-12-06 Thread Sachit Adhikari
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

[galaxy-user] Galaxy doesn't detect the file when we add dataset to a library under Manage data libraries

2012-12-11 Thread Sachit Adhikari
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?

[galaxy-user] How to add a built-in index for Tophat2?

2012-12-11 Thread Sachit Adhikari
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

[galaxy-user] How to add to add hg16 index into the build-in index / reference gnome list?

2012-12-12 Thread Sachit Adhikari
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

[galaxy-user] Error in TopHat

2012-12-19 Thread Sachit Adhikari
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

Re: [galaxy-user] Error in TopHat

2012-12-19 Thread Sachit Adhikari
: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

[galaxy-user] hg19 reference gnome for Tophat2

2013-02-12 Thread Sachit Adhikari
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

Re: [galaxy-user] hg19 reference gnome for Tophat2

2013-02-12 Thread Sachit Adhikari
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

[galaxy-user] Regarding galaxy wrappers: lumi, DESeq edgeR

2013-07-07 Thread Sachit Adhikari
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

Re: [galaxy-user] Regarding galaxy wrappers: lumi, DESeq edgeR

2013-07-08 Thread Sachit Adhikari
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

[galaxy-user] Rename tool output file in Galaxy

2013-07-23 Thread Sachit Adhikari
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

[galaxy-user] Rename tool output file in Galaxy

2013-07-23 Thread Sachit Adhikari
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

Re: [galaxy-user] Rename tool output file in Galaxy

2013-07-24 Thread Sachit Adhikari
, 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

Re: [galaxy-user] Rename tool output file in Galaxy

2013-07-24 Thread Sachit Adhikari
...@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

Re: [galaxy-user] Rename tool output file in Galaxy

2013-07-24 Thread Sachit Adhikari
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

[galaxy-user] Illumina Methylation tool in toolshed

2013-07-29 Thread Sachit Adhikari
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

Re: [galaxy-user] Illumina Methylation tool in toolshed

2013-07-29 Thread Sachit Adhikari
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