print out workflow execution commands!
Hi everyone, Is there an easy way to view/save/print out the executed commands and their parameters for a workflow? I want to see what is going on for certain steps in my workflow. Regards, Hak
Hi Hak, Yes, you can get all of the information saved for a particular workflow - in the abstract, not a particular workflow execution - by going to 'Download or Export' in the workflow menu, then click "Download to File". This will give you a .ga file which contains the steps in JSON format, which is fairly human readable. If you're asking for the actual command lines executed, you'll have to dig in the database a little bit to find the exact jobs you've executed and grab the command line from there, as this information isn't tied to the workflow itself -- at least, not directly. -Dannon On Tue, Apr 30, 2013 at 3:05 PM, Hakeem Almabrazi <halmabrazi@idtdna.com>wrote:
Hi everyone,****
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Is there an easy way to view/save/print out the executed commands and their parameters for a workflow? I want to see what is going on for certain steps in my workflow.****
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Regards,****
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Hak****
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___________________________________________________________ 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/
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Yes, I am actually looking for the actual command lines that were executed. I would like to know exactly how these tools are called so I can mimic that process from outside Galaxy env. I guess I have to dig into the database, but can you tell me what table(s) should I be looking at to find out that info? From: Dannon Baker [mailto:dannon.baker@gmail.com] Sent: Tuesday, April 30, 2013 2:11 PM To: Hakeem Almabrazi Cc: galaxy-dev@lists.bx.psu.edu List Subject: Re: [galaxy-dev] print out workflow execution commands! Hi Hak, Yes, you can get all of the information saved for a particular workflow - in the abstract, not a particular workflow execution - by going to 'Download or Export' in the workflow menu, then click "Download to File". This will give you a .ga file which contains the steps in JSON format, which is fairly human readable. If you're asking for the actual command lines executed, you'll have to dig in the database a little bit to find the exact jobs you've executed and grab the command line from there, as this information isn't tied to the workflow itself -- at least, not directly. -Dannon On Tue, Apr 30, 2013 at 3:05 PM, Hakeem Almabrazi <halmabrazi@idtdna.com<mailto:halmabrazi@idtdna.com>> wrote: Hi everyone, Is there an easy way to view/save/print out the executed commands and their parameters for a workflow? I want to see what is going on for certain steps in my workflow. Regards, Hak ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
You'll want the job table, and the field is command_line. On Tue, Apr 30, 2013 at 3:26 PM, Hakeem Almabrazi <halmabrazi@idtdna.com>wrote:
Yes, I am actually looking for the actual command lines that were executed. I would like to know exactly how these tools are called so I can mimic that process from outside Galaxy env. I guess I have to dig into the database, but can you tell me what table(s) should I be looking at to find out that info?****
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****
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*From:* Dannon Baker [mailto:dannon.baker@gmail.com] *Sent:* Tuesday, April 30, 2013 2:11 PM *To:* Hakeem Almabrazi *Cc:* galaxy-dev@lists.bx.psu.edu List *Subject:* Re: [galaxy-dev] print out workflow execution commands!****
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Hi Hak,****
** **
Yes, you can get all of the information saved for a particular workflow - in the abstract, not a particular workflow execution - by going to 'Download or Export' in the workflow menu, then click "Download to File". This will give you a .ga file which contains the steps in JSON format, which is fairly human readable.****
** **
If you're asking for the actual command lines executed, you'll have to dig in the database a little bit to find the exact jobs you've executed and grab the command line from there, as this information isn't tied to the workflow itself -- at least, not directly.****
** **
-Dannon****
** **
** **
On Tue, Apr 30, 2013 at 3:05 PM, Hakeem Almabrazi <halmabrazi@idtdna.com> wrote:****
Hi everyone,****
****
Is there an easy way to view/save/print out the executed commands and their parameters for a workflow? I want to see what is going on for certain steps in my workflow.****
****
Regards,****
****
Hak****
****
****
___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/****
** **
Thank You Danno, I will give it a try. By the way, is there a way to run a workflow and create a new history every time new data sets (fastq) is available programmatically? I have looked at the scripts at the ~api/ (ie. Example_watch, workflow_excute) scripts but I do not think these scripts can create a new history every time they get executed unless I am totally off. Regards From: Dannon Baker [mailto:dannon.baker@gmail.com] Sent: Tuesday, April 30, 2013 2:48 PM To: Hakeem Almabrazi Cc: galaxy-dev@lists.bx.psu.edu List Subject: Re: [galaxy-dev] print out workflow execution commands! You'll want the job table, and the field is command_line. On Tue, Apr 30, 2013 at 3:26 PM, Hakeem Almabrazi <halmabrazi@idtdna.com<mailto:halmabrazi@idtdna.com>> wrote: Yes, I am actually looking for the actual command lines that were executed. I would like to know exactly how these tools are called so I can mimic that process from outside Galaxy env. I guess I have to dig into the database, but can you tell me what table(s) should I be looking at to find out that info? From: Dannon Baker [mailto:dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>] Sent: Tuesday, April 30, 2013 2:11 PM To: Hakeem Almabrazi Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> List Subject: Re: [galaxy-dev] print out workflow execution commands! Hi Hak, Yes, you can get all of the information saved for a particular workflow - in the abstract, not a particular workflow execution - by going to 'Download or Export' in the workflow menu, then click "Download to File". This will give you a .ga file which contains the steps in JSON format, which is fairly human readable. If you're asking for the actual command lines executed, you'll have to dig in the database a little bit to find the exact jobs you've executed and grab the command line from there, as this information isn't tied to the workflow itself -- at least, not directly. -Dannon On Tue, Apr 30, 2013 at 3:05 PM, Hakeem Almabrazi <halmabrazi@idtdna.com<mailto:halmabrazi@idtdna.com>> wrote: Hi everyone, Is there an easy way to view/save/print out the executed commands and their parameters for a workflow? I want to see what is going on for certain steps in my workflow. Regards, Hak ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Yep, you can do this. In example_watch_folder.py, ~line 65, notice that the payload for the workflow post includes a 'history' key, which is the name of newly created history. In this particular example, it just names it "<Dataset Name> - <Workflow Name>", but you could use anything there. On Tue, Apr 30, 2013 at 5:22 PM, Hakeem Almabrazi <halmabrazi@idtdna.com>wrote:
Thank You Danno,****
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I will give it a try. By the way, is there a way to run a workflow and create a new history every time new data sets (fastq) is available programmatically? I have looked at the scripts at the ~api/ (ie. Example_watch, workflow_excute) scripts but I do not think these scripts can create a new history every time they get executed unless I am totally off.****
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Regards****
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*From:* Dannon Baker [mailto:dannon.baker@gmail.com] *Sent:* Tuesday, April 30, 2013 2:48 PM
*To:* Hakeem Almabrazi *Cc:* galaxy-dev@lists.bx.psu.edu List *Subject:* Re: [galaxy-dev] print out workflow execution commands!****
** **
You'll want the job table, and the field is command_line.****
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On Tue, Apr 30, 2013 at 3:26 PM, Hakeem Almabrazi <halmabrazi@idtdna.com> wrote:****
Yes, I am actually looking for the actual command lines that were executed. I would like to know exactly how these tools are called so I can mimic that process from outside Galaxy env. I guess I have to dig into the database, but can you tell me what table(s) should I be looking at to find out that info?****
****
****
****
*From:* Dannon Baker [mailto:dannon.baker@gmail.com] *Sent:* Tuesday, April 30, 2013 2:11 PM *To:* Hakeem Almabrazi *Cc:* galaxy-dev@lists.bx.psu.edu List *Subject:* Re: [galaxy-dev] print out workflow execution commands!****
****
Hi Hak,****
****
Yes, you can get all of the information saved for a particular workflow - in the abstract, not a particular workflow execution - by going to 'Download or Export' in the workflow menu, then click "Download to File". This will give you a .ga file which contains the steps in JSON format, which is fairly human readable.****
****
If you're asking for the actual command lines executed, you'll have to dig in the database a little bit to find the exact jobs you've executed and grab the command line from there, as this information isn't tied to the workflow itself -- at least, not directly.****
****
-Dannon****
****
****
On Tue, Apr 30, 2013 at 3:05 PM, Hakeem Almabrazi <halmabrazi@idtdna.com> wrote:****
Hi everyone,****
****
Is there an easy way to view/save/print out the executed commands and their parameters for a workflow? I want to see what is going on for certain steps in my workflow.****
****
Regards,****
****
Hak****
****
****
___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/****
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participants (2)
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Dannon Baker -
Hakeem Almabrazi