Re: [galaxy-dev] Workflow 'Input Dataset' Ressolution Issue

2015-10-11 Thread Marco Albuquerque
11, 2015 at 5:09 PM, Marco Albuquerque > wrote: > > Well, my Cloudman galaxy instance is installing 15.07 revision > 990501d2d9. > > > > Is there maybe a different revision I should be using? > > > > Marco > > > > On Sun, Oct 11, 2015 at 11:03 AM, Jo

Re: [galaxy-dev] Workflow 'Input Dataset' Ressolution Issue

2015-10-11 Thread Marco Albuquerque
es/776. Is it possible > that upgrading Galaxy to the latest 15.07 fixes the issue? > > On Thu, Oct 8, 2015 at 7:40 PM, Marco Albuquerque > wrote: > > Hello Galaxy Dev, > > > > Consider the workflow found in 'Strelka_Workflow_Sequential'

Re: [galaxy-dev] Parallelism using metadata

2015-03-03 Thread Marco Albuquerque
central/src/0468d285f89c799559926c94f3 >00c42d05e8c47a/test/api/test_workflows.py?at=default#cl-544). > >Thanks again, >-John > > >On Fri, Feb 27, 2015 at 10:04 PM, Marco Albuquerque > wrote: >> Hello Galaxy Dev, >> >> I have a question regarding parallel

[galaxy-dev] Parallelism using metadata

2015-03-02 Thread Marco Albuquerque
Hello Galaxy Dev, I have a question regarding parallelism on a BAM file. I have currently implemented 3 split options for the BAM datatype 1) by_rname -> splits the bam into files based on the chromosome 2) by_interval -> splits the bam into files based on a defined bp length, and does so acros

[galaxy-dev] Fasta Datatype Adjustments

2015-01-19 Thread Marco Albuquerque
Hello Galaxy, I have a small dilemma regarding the fasta datatype. Currently, to my knowledge, the fasta datatype does not specify any metadata. I was curious how I should go about changing the fasta datatype if I wanted to include the .fai and .dict as metadata? Basically I want to avoid unneces

[galaxy-dev] Tool Development DELLY

2015-01-09 Thread Marco Albuquerque
Hello Galaxy, I'm currently working on adding some tools and am having an issue with DELLY. So, I am under the impression that BAM indexing happens automatically when a BAM is uploaded. However there is no associated dataset_i.dat.bai file in the file location in my local instance of galaxy. The