[galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Ryan G
Hi all - I've got a bunch of fatsq files uploaded into a data library in Galaxy. The underlying files is gzipped however Galaxy strips the .gz from the filename and displays it as .fastq. When the python wrapper rgFastQC.py gets called, it correctly sees the fastq.gz file. The wrapper creates a

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Peter Cock
Hi Ryan, The problem isn't Galaxy stripping the extension, rather Galaxy is actually decompressing the file as part of the upload process. Unfortunately (and there is an open Trello enhancement request on this), Galaxy does not support sorting any of the defined datatypes in compressed form

Re: [galaxy-dev] No API way to delete a galaxy data library folder?

2015-01-12 Thread Dooley, Damion
Hi Martin - Following up on this - I think your API folder delete commit is : https://bitbucket.org/galaxy/galaxy-central/commits/8f76a6abc5d7d5c98b6c148c4cfe75cc1c159e90 ? I was wondering how to find out more about this API call. Not knowing the guts of the Galaxy API code much, is it a

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Ryan G
To (I think) fix this, I changed line 50 in rgFastQC.py from infname = self.opts.inputfilename to infname = self.opts.input This will force FastQC to look at the real file and not the renamed dataset. On Mon, Jan 12, 2015 at 12:20 PM, Ryan G ngsbioinformat...@gmail.com wrote: Yes, I'm doing

Re: [galaxy-dev] Partial automation for generating those twisty R dependency tool shed installation sequences

2015-01-12 Thread Ross
Hi Björn, I'm a bit old fashioned and think I prefer a proper Galaxy tool rather than a notebook :) so I've set up a temporary demonstration/test site of a toolfactory generated tool that does what I think I need - can some kind soul please test it and let me know how it goes ? If it's useful, it

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Peter Cock
Hi Ryan, That is the workaround I am using, which means keeping an uncompressed copy of the FASTQ file on our main storage from where Galaxy can see it (for people to use within their histories). From a long term storage perspective this is not ideal - so I am keen for better handling of gzipped

Re: [galaxy-dev] Tool Development DELLY

2015-01-12 Thread Peter Cock
Hi Marco, No problem - I originally copied the metadata access trick from one of the Galaxy dev-team's tool anyway. Maybe we need to add this to the wiki... Peter On Tuesday, January 13, 2015, Marco Albuquerque marcoalbuquerque@gmail.com wrote: Hi Peter, I was unaware of how to access

[galaxy-dev] Data manager .loc file not installing in correct place

2015-01-12 Thread Jeremy Liu
Galaxy Devs, I have a (semi) working data manager and I'm stuck on what exactly is going wrong. Most of it appears to be working properly, the intended file (pouya_test_motifs.bed.bgz) is being downloaded to the right directory (/galaxy-dist/tool-data/motifs). However, the .loc file that

[galaxy-dev] Display of file content in a combobox

2015-01-12 Thread christof.piet...@kws.com
Hello, I'd like to display the unique column content of a file in a combobox to give the user the possibility to select factor levels for subsequent analyses, e.g. for combining related factor levels in a meta-analyses. Unfortunately, I failed to connect the tool that reads out the factor levels

Re: [galaxy-dev] Galaxy Bioblend option for importing dataset into a library? (Nicola Soranzo)

2015-01-12 Thread Dooley, Damion
Hi Damion, I finally got to implement this, see method copy_from_dataset() in this commit: https://github.com/afgane/bioblend/commit/bc6b7cb71abb25aa109b85b1ff24e73aadac5ce4 Thanks Nicola! Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Ryan G
Galaxy is not decompressing the file. The file is linked to on the filesystem. On Mon, Jan 12, 2015 at 10:28 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Ryan, The problem isn't Galaxy stripping the extension, rather Galaxy is actually decompressing the file as part of the upload

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Peter Cock
Ah. Then this is more subtle... are you using the library import option where Galaxy just symlinks to existing files? I thought that was not possible with gzipped files (for the reasons given below). Perhaps this is not being blocked, leading to the confused state you're seeing? Peter On Mon,

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Ryan G
Yes, I'm doing a link to file on file system when doing a library import. Does this mean I should link to the the uncompressed file? On Mon, Jan 12, 2015 at 12:14 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Ah. Then this is more subtle... are you using the library import option where