Where to find the toolconfig parser code?
Quick question to you devs, I need to find the code where the tool configs are parsed ... especially the "free-text" if-else clauses in the command-tag. Could someone point me to the file? TIA // Samuel -- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se
Samuel, Look at the parse(0 method in the Tool class in ~/lib/galaxy/tools/__init__.py for most of it. You should be able to find everything you need from there. Greg Von Kuster On Jul 22, 2011, at 9:41 AM, Samuel Lampa wrote:
Quick question to you devs,
I need to find the code where the tool configs are parsed ... especially the "free-text" if-else clauses in the command-tag.
Could someone point me to the file?
TIA // Samuel
-- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Ah, thanks! I somehow missed that file altogether ... // Samuel On 07/22/2011 03:59 PM, Greg Von Kuster wrote:
Samuel,
Look at the parse(0 method in the Tool class in ~/lib/galaxy/tools/__init__.py for most of it. You should be able to find everything you need from there.
Greg Von Kuster
On Jul 22, 2011, at 9:41 AM, Samuel Lampa wrote:
Quick question to you devs,
I need to find the code where the tool configs are parsed ... especially the "free-text" if-else clauses in the command-tag.
Could someone point me to the file?
TIA // Samuel
-- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
-- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se
One follow up question then: The #if#else syntax, in for example this tool example: ... <command interpreter="python"> sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} #if $source.index_source == "history": --ref_file=$source.ref_file #else --ref_file="None" #end if --output1=$output1 --index_dir=${GALAXY_DATA_INDEX_DIR} </command> <inputs> ... ... is that something that you galaxy parses itself (tried to grep for some matching-code, but found nothing so far), or are that some python preprocessor directives? Best // Samuel On 07/22/2011 04:45 PM, Samuel Lampa wrote:
Ah, thanks! I somehow missed that file altogether ...
// Samuel
On 07/22/2011 03:59 PM, Greg Von Kuster wrote:
Samuel,
Look at the parse(0 method in the Tool class in ~/lib/galaxy/tools/__init__.py for most of it. You should be able to find everything you need from there.
Greg Von Kuster
On Jul 22, 2011, at 9:41 AM, Samuel Lampa wrote:
Quick question to you devs,
I need to find the code where the tool configs are parsed ... especially the "free-text" if-else clauses in the command-tag.
Could someone point me to the file?
TIA // Samuel
-- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
-- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se
On Fri, Jul 22, 2011 at 3:50 PM, Samuel Lampa <samuel.lampa@scilifelab.uu.se> wrote:
One follow up question then:
The #if#else syntax, in for example this tool example:
...
... is that something that you galaxy parses itself (tried to grep for some matching-code, but found nothing so far), or are that some python preprocessor directives?
Best // Samuel
It is a Python template language called Cheetah, see for eg: http://www.cheetahtemplate.org/docs/users_guide_html/ Peter
On 07/22/2011 04:53 PM, Peter Cock wrote:
On Fri, Jul 22, 2011 at 3:50 PM, Samuel Lampa <samuel.lampa@scilifelab.uu.se> wrote:
The #if#else syntax, in for example this tool example:
<snip>
... is that something that you galaxy parses itself (tried to grep for some matching-code, but found nothing so far), or are that some python preprocessor directives?
It is a Python template language called Cheetah, see for eg: http://www.cheetahtemplate.org/docs/users_guide_html/
Peter
Ah, IC, big thanks! :) // Samuel -- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se
participants (3)
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Greg Von Kuster -
Peter Cock -
Samuel Lampa