Re: [galaxy-dev] Batch limit on Wokflows
for f in files:if '_R1.fastq' in f: f2 = f.replace('_R1.fastq','_R2.fastq') data['ds_map'][get_workflow_step(myKey, galaxyURL, workflow_id, 'FASTQ Input (#1)')] = {'src':'ldda', 'id':files[f] } data['ds_map'][get_workflow_step(myKey, galaxyURL, workflow_id, 'FASTQ Input (#2)')] = {'src':'ldda', 'id':files[f2] } #History will be using PREFIX-FILENAME format data['history'] = "%s%s" % ( historyPrefix,f.split('/')[-1] ) print '---' print "Preparing workflow for :\n%s\n" % f if options.test:print data else:url = "" % galaxyURLsubmit( myKey, url, data )if __name__ == '__main__': main()/codeOn May 25, 2012, at 06:15 AM, Geert Vandeweyer geert.vandewey...@ua.ac.be wrote:I'm looking for a workflow of : Forward reads.fastq = QC = map = etc Reverse reads.fastq = and would like to specify pairs of files (from MiSeq) in the batch workflow interface. I'm currently looking into interlacing the files outside of galaxy before uploading. Then I can de-interlace as the first step, but this is redundant, as we get seperate files to start. Best regards, Geert On 05/25/2012 02:12 PM, Dannon Baker wrote: Batch mode is currently only allowed for a single input dataset step, so the others are intentionally disabled upon toggling the first one on. We do, however, plan to eventually expand this to allow for pairwise/etc input sets. Out of curiosity, which behavior is it that you're looking for? -Dannon On May 25, 2012, at 8:03 AM, Geert Vandeweyer wrote: Is it possible to use multiple 'input dataset' steps in a single workflow in batch? If I have two, I can only select batch input on one of them. If one is open, the other toggle button does not respond. Thanks, Geert On 02/14/2012 09:55 PM, Petit III, Robert A. wrote: Thats it! Consider this resolved, and total operator error. I tried using the 'Input Dataset' step, and am no longer having issues. Thanks for the help Dannon. ____________ From: Petit III, Robert A. Sent: Tuesday, February 14, 2012 3:49 PM To: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Batch limit on Wokflows Workflow is beginning directly with a tool. An example test workflow I've been trying is, I have 20 fasta files, and the workflow has only the FASTA-to-Tabular tool. Thanks, Robert From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, February 14, 2012 3:33 PM To: Petit III, Robert A. Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Batch limit on Wokflows I hadn't had a chance to follow up again yet, but in your workflow, are you using an Input Dataset step, or do you have the workflow beginning directly with a tool? -Dannon On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote: Here's the latest. I have tested this on Chrome, Firefox, and IE. I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or less datasets in the history, but as soon as I add a 20th I can no longer run a workflow on multiple datasets. Are there any known issues running galaxy on Ubuntu 10.04? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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/ --Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscr
Re: [galaxy-dev] Batch limit on Wokflows
Is it possible to use multiple 'input dataset' steps in a single workflow in batch? If I have two, I can only select batch input on one of them. If one is open, the other toggle button does not respond. Thanks, Geert On 02/14/2012 09:55 PM, Petit III, Robert A. wrote: Thats it! Consider this resolved, and total operator error. I tried using the 'Input Dataset' step, and am no longer having issues. Thanks for the help Dannon. From: Petit III, Robert A. Sent: Tuesday, February 14, 2012 3:49 PM To: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Batch limit on Wokflows Workflow is beginning directly with a tool. An example test workflow I've been trying is, I have 20 fasta files, and the workflow has only the FASTA-to-Tabular tool. Thanks, Robert From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, February 14, 2012 3:33 PM To: Petit III, Robert A. Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Batch limit on Wokflows I hadn't had a chance to follow up again yet, but in your workflow, are you using an Input Dataset step, or do you have the workflow beginning directly with a tool? -Dannon On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote: Here's the latest. I have tested this on Chrome, Firefox, and IE. I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or less datasets in the history, but as soon as I add a 20th I can no longer run a workflow on multiple datasets. Are there any known issues running galaxy on Ubuntu 10.04? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ 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] Batch limit on Wokflows
I'm looking for a workflow of : Forward reads.fastq = QC = map = etc Reverse reads.fastq = and would like to specify pairs of files (from MiSeq) in the batch workflow interface. I'm currently looking into interlacing the files outside of galaxy before uploading. Then I can de-interlace as the first step, but this is redundant, as we get seperate files to start. Best regards, Geert On 05/25/2012 02:12 PM, Dannon Baker wrote: Batch mode is currently only allowed for a single input dataset step, so the others are intentionally disabled upon toggling the first one on. We do, however, plan to eventually expand this to allow for pairwise/etc input sets. Out of curiosity, which behavior is it that you're looking for? -Dannon On May 25, 2012, at 8:03 AM, Geert Vandeweyer wrote: Is it possible to use multiple 'input dataset' steps in a single workflow in batch? If I have two, I can only select batch input on one of them. If one is open, the other toggle button does not respond. Thanks, Geert On 02/14/2012 09:55 PM, Petit III, Robert A. wrote: Thats it! Consider this resolved, and total operator error. I tried using the 'Input Dataset' step, and am no longer having issues. Thanks for the help Dannon. From: Petit III, Robert A. Sent: Tuesday, February 14, 2012 3:49 PM To: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Batch limit on Wokflows Workflow is beginning directly with a tool. An example test workflow I've been trying is, I have 20 fasta files, and the workflow has only the FASTA-to-Tabular tool. Thanks, Robert From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, February 14, 2012 3:33 PM To: Petit III, Robert A. Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Batch limit on Wokflows I hadn't had a chance to follow up again yet, but in your workflow, are you using an Input Dataset step, or do you have the workflow beginning directly with a tool? -Dannon On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote: Here's the latest. I have tested this on Chrome, Firefox, and IE. I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or less datasets in the history, but as soon as I add a 20th I can no longer run a workflow on multiple datasets. Are there any known issues running galaxy on Ubuntu 10.04? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ 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] Batch limit on Wokflows
Here's the latest. I have tested this on Chrome, Firefox, and IE. I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or less datasets in the history, but as soon as I add a 20th I can no longer run a workflow on multiple datasets. Are there any known issues running galaxy on Ubuntu 10.04? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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] Batch limit on Wokflows
I hadn't had a chance to follow up again yet, but in your workflow, are you using an Input Dataset step, or do you have the workflow beginning directly with a tool? -Dannon On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote: Here's the latest. I have tested this on Chrome, Firefox, and IE. I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or less datasets in the history, but as soon as I add a 20th I can no longer run a workflow on multiple datasets. Are there any known issues running galaxy on Ubuntu 10.04? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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] Batch limit on Wokflows
Workflow is beginning directly with a tool. An example test workflow I've been trying is, I have 20 fasta files, and the workflow has only the FASTA-to-Tabular tool. Thanks, Robert From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, February 14, 2012 3:33 PM To: Petit III, Robert A. Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Batch limit on Wokflows I hadn't had a chance to follow up again yet, but in your workflow, are you using an Input Dataset step, or do you have the workflow beginning directly with a tool? -Dannon On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote: Here's the latest. I have tested this on Chrome, Firefox, and IE. I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or less datasets in the history, but as soon as I add a 20th I can no longer run a workflow on multiple datasets. Are there any known issues running galaxy on Ubuntu 10.04? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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] Batch limit on Wokflows
Thats it! Consider this resolved, and total operator error. I tried using the 'Input Dataset' step, and am no longer having issues. Thanks for the help Dannon. From: Petit III, Robert A. Sent: Tuesday, February 14, 2012 3:49 PM To: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Batch limit on Wokflows Workflow is beginning directly with a tool. An example test workflow I've been trying is, I have 20 fasta files, and the workflow has only the FASTA-to-Tabular tool. Thanks, Robert From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, February 14, 2012 3:33 PM To: Petit III, Robert A. Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Batch limit on Wokflows I hadn't had a chance to follow up again yet, but in your workflow, are you using an Input Dataset step, or do you have the workflow beginning directly with a tool? -Dannon On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote: Here's the latest. I have tested this on Chrome, Firefox, and IE. I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or less datasets in the history, but as soon as I add a 20th I can no longer run a workflow on multiple datasets. Are there any known issues running galaxy on Ubuntu 10.04? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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] Batch limit on Wokflows
Sorry for the delay, but I am using a galaxy-dist clone, and have updated to revision 26920e20157f+ tip. I'm still receiving the same issue with the revision. Maybe I should try out galaxy-central? Thanks, Robert From: Dannon Baker [dannonba...@me.com] Sent: Friday, February 10, 2012 11:50 AM To: Petit III, Robert A. Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Batch limit on Wokflows What revision is your Galaxy instance at? I'm not seeing this behavior on tip with a simple test, it may have been something we've fixed in a more recent revision. -Dannon On Feb 10, 2012, at 11:14 AM, Petit III, Robert A. wrote: Hi there, I've run into an issue on my local galaxy install. When I have 20 or more datasets in my history, I no longer get the option to 'Enable/Disable selection of multiple input files...' I instead get a broken drop down list. I say broken because its as though the drop down list and input box have merged together. Is there a setting I need to change to correct this? Thanks Robert This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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] Batch limit on Wokflows
OK, I've tried the latest revision og 'Galaxy-Central' and am still running into the same issue, when I try to run a work flow when there are 20+ datasets in my history. I might try setting it up on another machine to see if I run into the same issue. Thanks, Robert From: Petit III, Robert A. Sent: Monday, February 13, 2012 11:05 AM To: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Batch limit on Wokflows Sorry for the delay, but I am using a galaxy-dist clone, and have updated to revision 26920e20157f+ tip. I'm still receiving the same issue with the revision. Maybe I should try out galaxy-central? Thanks, Robert From: Dannon Baker [dannonba...@me.com] Sent: Friday, February 10, 2012 11:50 AM To: Petit III, Robert A. Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Batch limit on Wokflows What revision is your Galaxy instance at? I'm not seeing this behavior on tip with a simple test, it may have been something we've fixed in a more recent revision. -Dannon On Feb 10, 2012, at 11:14 AM, Petit III, Robert A. wrote: Hi there, I've run into an issue on my local galaxy install. When I have 20 or more datasets in my history, I no longer get the option to 'Enable/Disable selection of multiple input files...' I instead get a broken drop down list. I say broken because its as though the drop down list and input box have merged together. Is there a setting I need to change to correct this? Thanks Robert This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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] Batch limit on Wokflows
What revision is your Galaxy instance at? I'm not seeing this behavior on tip with a simple test, it may have been something we've fixed in a more recent revision. -Dannon On Feb 10, 2012, at 11:14 AM, Petit III, Robert A. wrote: Hi there, I've run into an issue on my local galaxy install. When I have 20 or more datasets in my history, I no longer get the option to 'Enable/Disable selection of multiple input files...' I instead get a broken drop down list. I say broken because its as though the drop down list and input box have merged together. Is there a setting I need to change to correct this? Thanks Robert This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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/
