[galaxy-dev] Picard installation problem

2011-08-14 Thread colin molter
Hello all, I get troubles installing Picard. In short is there a dedicated link with precise instructions on how to install it on Galaxy? I spent hours trying to install it and if I made a subtle step forward in the installation, I am still stuck with exceptions when trying to run any picard tool.

Re: [galaxy-dev] Picard installation problem

2011-08-14 Thread Brad Chapman
Colin; > Second -and still unsolved- problem: When i try to run a picard tool, I get > the following exception: > > File "/home/hg/Galaxy/galaxy-dist/tools/picard/picard_wrapper.py", line 40 > class PicardBase(): > ^ > SyntaxError: invalid syntax What version of Python

Re: [galaxy-dev] Picard installation problem

2011-08-14 Thread colin molter
If i type python in a terminal, it says that it uses the version 2.6.7. And it succeed in creating a class Test(). is it possible that my galaxy distribution is using an older version? is there a way to check what python version does galaxy use? thanks colin 2011/8/14 Brad Chapman > Colin; > >

Re: [galaxy-dev] Picard installation problem

2011-08-14 Thread Ross
Hi, Colin. Sorry you are having such problems. There's a lot of detailed documented that's just not yet written. As you discovered, Picard tools expect the individual Picard jar files to be in tool-data/shared/jars/ eg in one of the tools like rgPicardMarkDupes.xml you'll see -j "${GALAXY_DATA_I

Re: [galaxy-dev] Picard installation problem

2011-08-14 Thread Brad Chapman
Colin; > If i type python in a terminal, it says that it uses the version 2.6.7. > And it succeed in creating a class Test(). > > is it possible that my galaxy distribution is using an older version? is > there a way to check what python version does galaxy use? Unless you've modified the run.sh

Re: [galaxy-dev] trackster reference genome

2011-08-14 Thread Jeremy Goecks
Colin, > How is it possible to preinstall a reference genome for trackster (hg19) > within galaxy. > > i tried to find a dedicated help page but could not find any. Could you > please link me to relevant information? See the section titled 'Setup for local instances' on this page: http://wiki

Re: [galaxy-dev] Extract Genomic DNA insisting on build for GFF3 file

2011-08-14 Thread Jeremy Goecks
> > Great. Could you try that example on the latest galaxy-central please? > I have revision 06f0bca6de24 and get the following error using the > steps given earlier: > > Traceback (most recent call last): > File > "/home/pjcock/repositories/galaxy-central/tools/extract/extract_genomic_dna.py",

Re: [galaxy-dev] Extract Genomic DNA insisting on build for GFF3 file

2011-08-14 Thread Jeremy Goecks
> I think I've found another problem in exploring possible workarounds, > > 1. Goto http://usegalaxy.org (or a local Galaxy running galaxy-dist or > galaxy-central) > > 2. Import this GFF3 file, > ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans_Kin4_M_uid58009/NC_005213.gff > > 3.

Re: [galaxy-dev] Extract Genomic DNA insisting on build for GFF3 file

2011-08-14 Thread Jeremy Goecks
> Well, sort of. After converting that GFF3 file into BED, the strand column > isn't set in the metadata. That seems important! We'll look into this. > Also a point of clarification, I had the wrong URL for the FASTA file. > > This is the whole genome, although to actually proceed with this > ex

[galaxy-dev] Whole genome simulation with dwgsim

2011-08-14 Thread Nils Homer
I wanted to plug two tools that we have wrapped up for Galaxy: whole genome simulation of NGS reads, as well as the evaluation of the resulting mappings of those reads. This could be very useful for those that want to evaluate mapping algorithms, or experiment with simulated NGS data. Check out

Re: [galaxy-dev] filter

2011-08-14 Thread KOH Jia Yu Jayce
Hi thanks, but what sanitizer option should I set it to? -Original Message- From: Bossers, Alex [mailto:alex.boss...@wur.nl] Sent: Thursday, August 04, 2011 3:11 PM To: KOH Jia Yu Jayce Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: RE: filter If I understand it correctly; You have to check