[galaxy-dev] email change

Hi galaxy team, I changed my email address in my personal data settings. But it seems not working. Deeps ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other

[galaxy-dev] index file

Hi galaxy team, How can we make an index file for a presorted bam file using galaxy? Thanks, Deepthi ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy

[galaxy-dev] [Fwd: SAM to BAM tool for custom genome build]

---BeginMessage--- Hi Galaxy Team, I am using custom genome build for creating a sam file. When I am trying to use the SAM to BAM tool inside Sam Tools with option locally cached I am getting an error like Unspecified genome build, click the pencil icon in the history item to set the genome

[galaxy-dev] [Fwd: Tracking .bai files]

---BeginMessage--- Hai Galaxy Team, I have created a .sam file using my own tool. I used a custom genome that I added to the bowtie_indices.loc. I want to create another tool which will contain 3 steps, 1. samtool view (sam to bam conversion) 2. samtool sort (sorting bam file) 3. samtool index

[galaxy-dev] Tracking .bai files

Hai Galaxy Team, I have created a .sam file using my own tool. I used a custom genome that I added to the bowtie_indices.loc. I want to create another tool which will contain 3 steps, 1. samtool view (sam to bam conversion) 2. samtool sort (sorting bam file) 3. samtool index (creating .bai

[galaxy-dev] SAM to BAM tool for custom genome build

Hi Galaxy Team, I am using custom genome build for creating a sam file. When I am trying to use the SAM to BAM tool inside Sam Tools with option locally cached I am getting an error like Unspecified genome build, click the pencil icon in the history item to set the genome build. I added the

[galaxy-dev] New Tool - Can provide a template file to user

Hi all, I am trying to add a tool to galaxy. I want to collect some data from the user. The data may contain hundreds of records each has 7 or 8 fields. Either user can upload a spreadsheet for that or I shall provide a template file to fill up the data. When I checked there is no provision

[galaxy-dev] Adding New filetype

Hi Galaxy-Dev, I have a a special set of .txt files which contains some comments and tabular feilds. I want to make them as a different group so that I can list them without any other .txt files. I went through the Add New Data Type section.But I didnt get a clear idea of how to do it? The

[galaxy-dev] One tool ,multiple set of outputs

Hi all, Can I implement a tool which run 2 different algorithms and providing different set of output? Eg:Suppose I am having a tool named mytool which is running 2 different programs for 2 different conditions. Output of first program is a text file and fasta file and output of second

[galaxy-dev] dynamic_options

Hi all, Is there any help available which describes about the usage of dynamic_options? Is the code file should be a python executable or can we use perl? Thanks and regards, Deepthi ___ Please keep all replies on the list by using reply

[galaxy-dev] repeat tag

Hi all, This is a question about repeat tag. How can we pass the repeat tag parameters nested within another repeat tag to command tag? For example,I have a front end like the following conditional name=cond1 when value=something repeat name=rpt1. param1

[galaxy-dev] repeat tag

Hi all, This is a question about repeat tag. How can we pass the repeat tag parameters nested within another repeat tag to command tag? For example,I have a front end like the following conditional name=cond1 when value=something repeat name=rpt1. param1