18 May
2015
18 May
'15
2:08 p.m.
THANK YOU!!! :) The fundamental piece that I was missing at: https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes was the <command>someTool.sh $input1 ${os.path.join( input1.extra_files_path, 'results.txt' )} ${os.path.join( input1.extra_files_path, 'results.dat' )} $output1</command> It would be great if the documentation could be updated a bit for clarity on the importance of the '.extra_files_path', such as 'important: your tool needs to create this directory and store the additional files that you want there'. This is a big leap forward for me. I'll now get on to testing the other aspects of it. (still climbing the galaxy learning curve). thanks again! ~brian On Mon, May 18, 2015 at 2:39 PM, Daniel Blankenberg <dan@bx.psu.edu> wrote: > Hi Brian, > > In your example tool, you need to pass “${ test_cdt.files_path }" to your > perl script, which is a not-yet-existing directory for the files you want > to be part of the dataset’s extra files path. > Then you create that directory and place the files you want within that > directory. > > > > Thanks for using Galaxy, > > Dan > > > On May 18, 2015, at 2:02 PM, Brian Haas <bhaas@broadinstitute.org> wrote: > > > Hi Peter, > > > > I'm actually more confused now that I was when I started... I was able > to get your code working, focusing on the 'makeblastdb' with a nucleotide > fasta file. I figured that experimenting with this example would lead to > some key insights, particularly by dropping certain files that are stored > as extra-files area. I copied everything over as a new tool, made it a > new data type, and trimmed the blast.py code down to the bare essentials > for testing just the nucleotide makeblastdb functionality. However, > commenting out 'self.add_composite_file()' for various files had no effect > - the files were still being stored. I then make 'composite_type = None' > and it still stored the files to my dismay. > > > > Since I couldn't get my copy to work as I had expected, I went back over > to your 'blast.py' and just commented out the ''self.add_composite_file()' > lines and set 'composite_type = None' .... and no effect. > > > > Of course, I restarted galaxy after each modification, and could verify > that it was reading the new files and had byte-compiled the py mods. > > > > I'm clearly not grasping something fundamental here. I can't get my > code to bundle files, and I can't get your code to *not* bundle files. ;) > > > > Any ideas on where to go to troubleshoot this further? > > > > many thanks, > > > > ~brian > > > > ___________________________________________________________ > > 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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>