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.
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
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;
>
>
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
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
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
>
> 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",
> 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.
> 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
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
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
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