Re: [galaxy-user] using files produced by Barcode Splitter
I've had users make a similar request for the split files to appear in their history. I made my own wrapper to enable this behavior. It presents a list of barcodes from the barcode file input. Any barcodes the user selects will have the resulting files copied to the users history as new datasets. I uploaded my barcode splitter tool configs to the toolshed: http://toolshed.g2.bx.psu.edu/ as repository: barcode_splitter JJ Date: Mon, 18 Jul 2011 13:33:58 -0700 From: Jeremy Coate je...@cornell.edu To: David K Crossman dkcro...@uab.edu Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] using files produced by Barcode Splitter Message-ID: caa2bwd5ueraqeoueq97tfnhkwvhziq89whvr-oy04ov-k4j...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Thanks David, I had considered this possibility but, curiously, the files don't show up in the FastQ Groomer pull-down menu either. The original (multiplexed) data file that I split using the Barcode Splitter is there (and, incidentally, I ran FastQ Groomer on that before doing the barcode split), but none of the 3 files resulting from the splitter show up. Any other thoughts? It seems like the new files just aren't landing in my history, though I can look at them by clicking their links from the Barcode Splitter output. Jeremy On Mon, Jul 18, 2011 at 12:01 PM, David K Crossman dkcro...@uab.edu wrote: Jeremy, ** ** The files need to be groomed using the FastQ Groomer so that they will end up in the fastqsanger state. Then your files will show up in the pull-down menus. ** ** David ** ** ** ** *From:*galaxy-user-boun...@lists.bx.psu.edu [mailto: galaxy-user-boun...@lists.bx.psu.edu] *On Behalf Of *Jeremy Coate *Sent:* Monday, July 18, 2011 1:44 PM *To:*galaxy-user@lists.bx.psu.edu *Subject:* [galaxy-user] using files produced by Barcode Splitter ** ** I used the Barcode Splitter tool to split multiplexed RNA-Seq libraries into separate files. I would now like to map the reads from each of these fastq files to a reference genome. However, the fastq files generated by Barcode Splitter don't appear in the Fastq File pull-down menus within the the BWA or Bowtie launch pages. I'm probably missing something obvious, but what is the trick for making these files available for the mapping tools? Do I need to import them into my history somehow? ** ** Thanks! Jeremy ___ 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] using files produced by Barcode Splitter
Jeremy, Usually, the users saved the files to their local machine by clicking on the links, and then uploaded them again to the galaxy server. It can be possible to copy the link location, and paste it into the upload tools URL textarea. Ideally, it would be nice for the tool developer to be able to include a link in the html that would promote the file to a dataset in the current history. JJ On 7/19/11 3:08 PM, Jeremy Coate wrote: Thanks, Jim! I'll see if my limited Galaxy/bioinformatics skills can rise to the challenge of using your wrapper (I've never visited the tool shed before). Out of curiosity, how did people use the files generated by the barcode splitter without this? I'm assuming there was/is a way, but I'm not figuring it out. Jeremy On Tue, Jul 19, 2011 at 11:26 AM, Jim Johnson johns...@umn.edu mailto:johns...@umn.edu wrote: I've had users make a similar request for the split files to appear in their history. I made my own wrapper to enable this behavior. It presents a list of barcodes from the barcode file input. Any barcodes the user selects will have the resulting files copied to the users history as new datasets. I uploaded my barcode splitter tool configs to the toolshed: http://toolshed.g2.bx.psu.edu/ as repository: barcode_splitter JJ Date: Mon, 18 Jul 2011 13:33:58 -0700 From: Jeremy Coate je...@cornell.edu mailto:je...@cornell.edu To: David K Crossman dkcro...@uab.edu mailto:dkcro...@uab.edu Cc: galaxy-user@lists.bx.psu.edu mailto:galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu mailto:galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] using files produced by Barcode Splitter Message-ID: caa2bwd5ueraqeoueq97tfnhkwvhziq89whvr-oy04ov-k4j...@mail.gmail.com mailto:caa2bwd5ueraqeoueq97tfnhkwvhziq89whvr-oy04ov-k4j...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Thanks David, I had considered this possibility but, curiously, the files don't show up in the FastQ Groomer pull-down menu either. The original (multiplexed) data file that I split using the Barcode Splitter is there (and, incidentally, I ran FastQ Groomer on that before doing the barcode split), but none of the 3 files resulting from the splitter show up. Any other thoughts? It seems like the new files just aren't landing in my history, though I can look at them by clicking their links from the Barcode Splitter output. Jeremy On Mon, Jul 18, 2011 at 12:01 PM, David K Crossman dkcro...@uab.edu mailto:dkcro...@uab.edu wrote: Jeremy, ** ** The files need to be groomed using the FastQ Groomer so that they will end up in the fastqsanger state. Then your files will show up in the pull-down menus. ** ** David ** ** ** ** *From:* galaxy-user-boun...@lists.bx.psu.edu mailto:galaxy-user-boun...@lists.bx.psu.edu [mailto: galaxy-user-boun...@lists.bx.psu.edu mailto:galaxy-user-boun...@lists.bx.psu.edu] *On Behalf Of *Jeremy Coate *Sent:* Monday, July 18, 2011 1:44 PM *To:* galaxy-user@lists.bx.psu.edu mailto:galaxy-user@lists.bx.psu.edu *Subject:* [galaxy-user] using files produced by Barcode Splitter ** ** I used the Barcode Splitter tool to split multiplexed RNA-Seq libraries into separate files. I would now like to map the reads from each of these fastq files to a reference genome. However, the fastq files generated by Barcode Splitter don't appear in the Fastq File pull-down menus within the the BWA or Bowtie launch pages. I'm probably missing something obvious, but what is the trick for making these files available for the mapping tools? Do I need to import them into my history somehow? ** ** Thanks! Jeremy ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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] using files produced by Barcode Splitter
Ah ha - thanks. I was trying to click the link, but it kept crashing, presumably because the files are too big. The URL method seems to work, though. I agree that it would be nice if there was a way to bump the files directly into your history without the download/upload steps. Thanks again for the help. Jeremy On Tue, Jul 19, 2011 at 1:20 PM, Jim Johnson johns...@umn.edu wrote: Jeremy, Usually, the users saved the files to their local machine by clicking on the links, and then uploaded them again to the galaxy server. It can be possible to copy the link location, and paste it into the upload tools URL textarea. Ideally, it would be nice for the tool developer to be able to include a link in the html that would promote the file to a dataset in the current history. JJ On 7/19/11 3:08 PM, Jeremy Coate wrote: Thanks, Jim! I'll see if my limited Galaxy/bioinformatics skills can rise to the challenge of using your wrapper (I've never visited the tool shed before). Out of curiosity, how did people use the files generated by the barcode splitter without this? I'm assuming there was/is a way, but I'm not figuring it out. Jeremy On Tue, Jul 19, 2011 at 11:26 AM, Jim Johnson johns...@umn.edu wrote: I've had users make a similar request for the split files to appear in their history. I made my own wrapper to enable this behavior. It presents a list of barcodes from the barcode file input. Any barcodes the user selects will have the resulting files copied to the users history as new datasets. I uploaded my barcode splitter tool configs to the toolshed: http://toolshed.g2.bx.psu.edu/ as repository: barcode_splitter JJ Date: Mon, 18 Jul 2011 13:33:58 -0700 From: Jeremy Coate je...@cornell.edu je...@cornell.edu To: David K Crossman dkcro...@uab.edu dkcro...@uab.edu Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] using files produced by Barcode Splitter Message-ID: caa2bwd5ueraqeoueq97tfnhkwvhziq89whvr-oy04ov-k4j...@mail.gmail.com caa2bwd5ueraqeoueq97tfnhkwvhziq89whvr-oy04ov-k4j...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Thanks David, I had considered this possibility but, curiously, the files don't show up in the FastQ Groomer pull-down menu either. The original (multiplexed) data file that I split using the Barcode Splitter is there (and, incidentally, I ran FastQ Groomer on that before doing the barcode split), but none of the 3 files resulting from the splitter show up. Any other thoughts? It seems like the new files just aren't landing in my history, though I can look at them by clicking their links from the Barcode Splitter output. Jeremy On Mon, Jul 18, 2011 at 12:01 PM, David K Crossman dkcro...@uab.edu dkcro...@uab.edu wrote: Jeremy, ** ** The files need to be groomed using the FastQ Groomer so that they will end up in the fastqsanger state. Then your files will show up in the pull-down menus. ** ** David ** ** ** ** *From:* galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] *On Behalf Of *Jeremy Coate *Sent:* Monday, July 18, 2011 1:44 PM *To:* galaxy-user@lists.bx.psu.edu *Subject:* [galaxy-user] using files produced by Barcode Splitter ** ** I used the Barcode Splitter tool to split multiplexed RNA-Seq libraries into separate files. I would now like to map the reads from each of these fastq files to a reference genome. However, the fastq files generated by Barcode Splitter don't appear in the Fastq File pull-down menus within the the BWA or Bowtie launch pages. I'm probably missing something obvious, but what is the trick for making these files available for the mapping tools? Do I need to import them into my history somehow? ** ** Thanks! Jeremy ___ 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
Re: [galaxy-user] using files produced by Barcode Splitter
Jeremy, The files need to be groomed using the FastQ Groomer so that they will end up in the fastqsanger state. Then your files will show up in the pull-down menus. David From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jeremy Coate Sent: Monday, July 18, 2011 1:44 PM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] using files produced by Barcode Splitter I used the Barcode Splitter tool to split multiplexed RNA-Seq libraries into separate files. I would now like to map the reads from each of these fastq files to a reference genome. However, the fastq files generated by Barcode Splitter don't appear in the Fastq File pull-down menus within the the BWA or Bowtie launch pages. I'm probably missing something obvious, but what is the trick for making these files available for the mapping tools? Do I need to import them into my history somehow? Thanks! Jeremy ___ 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/
