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

2015-01-18 Thread John Chilton
Peter has already voted and if I recall correctly Ryan cannot access Trello - so this might be a waste to bring up - but here is a Trello card for voting on this issue and tracking progress https://trello.com/c/3RkTDnIn. To summarize previous discussion - this would be fantastic to have and

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

2015-01-13 Thread Ryan G
Agreed. On Mon, Jan 12, 2015 at 10:24 PM, Peter Cock p.j.a.c...@googlemail.com wrote: 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

[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 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] 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] 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