Hey, with the "tool file" line I got it working :) Thanks a lot. Could you answer the question regarding Tool Shed: "If I would use Tool Shed, could I skip all these manual steps? Is the installation of BWA with Tool Shed also this complicated or is it more simle?"
Best Moritz On 17 July 2013 09:51, Moritz Juchler <juch...@stud.uni-heidelberg.de>wrote: > Hey, > > no thats correct I did not use Tool Shed. If I would use it, could I skip > all these manual steps? Is the installation of BWA with Tool Shed also this > complicated or is it more simle? > > How did you not follow my steps :) I wrote down everything clearly, at > least thats what I was hoping. > > And no I didnt write this line " <tool file="sr_mapping/bwa_wrapper.**xml" > />" Thats the first time, I am seeing this tutorial :( I will try this > out right now > > Best > Moritz > > > On 17 July 2013 09:42, Hans-Rudolf Hotz <h...@fmi.ch> wrote: > >> Hi Moritz >> >> I am struggling to follow what exactly you have done. As far as I can >> see, you did not use the toolshed (http://wiki.galaxyproject.** >> org/Tool%20Shed <http://wiki.galaxyproject.org/Tool%20Shed>) to install >> the BWA alinger tool, but did all manually? >> >> If so, have you added the following line: >> >> <tool file="sr_mapping/bwa_wrapper.**xml" /> >> >> to the "tool_conf.xml" file, and restarted Galaxy? >> >> >> see also: >> http://wiki.galaxyproject.org/**Admin/Tools/Add%20Tool%**20Tutorial<http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial> >> >> >> >> Hope this helps >> Hans-Rudolf >> >> >> >> >> >> On 07/16/2013 08:35 PM, Moritz Juchler wrote: >> >>> Hello Ladies and Gentlemen, >>> >>> I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I >>> have to choose a bioinformatic pipeline management tool to find SNP's in >>> genomes from hcc patients. My decision was made in favor of galaxy. I >>> have a 64-bit openSuse 11.3 server. >>> I have installed Galaxy locally, since we have a) very large files >>> (>30GB per patient) and b) the data is protection sensitive. I kept >>> close to >>> http://wiki.galaxyproject.org/**Admin/Get%20Galaxy<http://wiki.galaxyproject.org/Admin/Get%20Galaxy> >>> Now I would like to run this bpipe pipeline: >>> http://pastebin.com/sZd5vfdL >>> And the first step is to align my genome to a _hg19 reference genome_ >>> >>> which I have locally under /genedata/human_genome_GRCh37/**. >>> >>> trr@portalmoritz:~> ls -l /genedata/human_genome_GRCh37/ >>> total 8486312 >>> -rw-r--r-- 1 trr root 3199905909 2013-06-25 16:44 hg19.fa >>> -rw-r--r-- 1 trr root 8591 2013-07-01 16:06 hg19.fa.amb >>> -rw-r--r-- 1 trr root 4040 2013-07-01 16:06 hg19.fa.ann >>> -rw-r--r-- 1 trr root 3137161344 2013-07-01 16:05 hg19.fa.bwt >>> -rw-r--r-- 1 trr root 784290318 2013-07-01 16:06 hg19.fa.pac >>> -rw-r--r-- 1 trr root 1568580688 2013-07-01 16:31 hg19.fa.sa >>> <http://hg19.fa.sa> >>> >>> >>> _bwa is installed and gives me:_ >>> >>> >>> trr@portalmoritz:~> bwa >>> Program: bwa (alignment via Burrows-Wheeler transformation) >>> Version: 0.7.5a-r405 >>> Contact: Heng Li <l...@sanger.ac.uk <mailto:l...@sanger.ac.uk>> >>> >>> >>> >>> Then I tried to follow this guide: >>> http://wiki.galaxyproject.org/**Admin/NGS%20Local%20Setup<http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup>to >>> get the >>> reference files and >>> http://wiki.galaxyproject.org/**Admin/Config/Tool%**20Dependencies<http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies> >>> . >>> >>> This is my _$PATH_ >>> >>> >>> trr@portalmoritz:~> echo $PATH >>> /home/trr/bin:/usr/local/bin:/**usr/bin:/bin:/usr/bin/X11:/** >>> usr/X11R6/bin:/usr/games:/**home/trr/bpipe-0.9.8/bin:/** >>> home/trr/bwa-0.7.5a:/home/trr/**samtools-0.1.19 >>> >>> >>> _In the universe_wsgi.ini I changed:_ >>> >>> >>> tool_dependency_dir = /home/trr/galaxy-dist/tool_**dependency_dir >>> debug = False >>> use_interactive = True >>> library_import_dir = /genedata/ >>> allow_library_path_paste = True >>> admin_users = ... >>> >>> >>> This is my _tool_dependency_dir:_ >>> >>> >>> trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa> ls -l >>> total 4 >>> drwxr-xr-x 3 trr users 4096 2013-07-16 14:28 0.7.4 >>> lrwxrwxrwx 1 trr users 6 2013-07-16 14:17 default -> 0.7.4/ >>> >>> >>> This is the_version folder of bwa:_ >>> >>> >>> trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4> >>> ls -l >>> total 8 >>> drwxr-xr-x 2 trr users 4096 2013-07-16 14:18 bin >>> -rw-r--r-- 1 trr users 47 2013-07-16 14:22 env.sh >>> >>> >>> This is the _content of env.sh:_ >>> >>> >>> trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4> >>> cat env.sh >>> PATH="/home/trr/bwa-0.7.5a/:$**PATH" >>> export PATH >>> >>> >>> And this is the _content of the bin folder:_ >>> >>> >>> trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4/bin> >>> ls -l >>> total 3896 >>> -rw-r--r-- 1 trr users 6098 2013-07-16 14:18 bamlite.c >>> -rw-r--r-- 1 trr users 3124 2013-07-16 14:18 bamlite.h >>> -rw-r--r-- 1 trr users 24816 2013-07-16 14:18 bamlite.o >>> -rw-r--r-- 1 trr users 11508 2013-07-16 14:18 bntseq.c >>> -rw-r--r-- 1 trr users 2557 2013-07-16 14:18 bntseq.h >>> -rw-r--r-- 1 trr users 37440 2013-07-16 14:18 bntseq.o >>> -rwxr-xr-x 1 trr users 998217 2013-07-16 14:18 bwa >>> -rw-r--r-- 1 trr users 24225 2013-07-16 14:18 bwa.1 >>> -rw-r--r-- 1 trr users 9416 2013-07-16 14:18 bwa.c >>> -rw-r--r-- 1 trr users 1381 2013-07-16 14:18 bwa.h >>> >>> .... >>> >>> >>> I got the xmls and .py from >>> https://bitbucket.org/galaxy/**galaxy-dist/src/da9d740fce31/** >>> tools/sr_mapping<https://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mapping>and >>> i didnt change them at all and put them into >>> ~/galaxy-dist/_tools/sr_**mapping_ (since they were missing in this >>> folder) >>> >>> bwa_color_wrapper.xml >>> bwa_wrapper.py >>> bwa_wrapper.xml >>> >>> >>> >>> I added _bwa_index_color.loc and bwa_index.loc_ to >>> ~galaxy-dist/_tool-data_ (they were missing as well, there/*were no*/ >>> >>> bwa_index_color.loc.sample or bwa_index.lox.sample files!!!) >>> >>> I only have this single line in both bwa_index_color.loc and >>> bwa_index.loc >>> >>> trr@portalmoritz:~/galaxy-**dist/tool-data> cat bwa_index_color.loc >>> #This is a sample file distributed with Galaxy that enables tools >>> # >>> #<unique_build_id> <dbkey> <display_name> <file_path> >>> hg19 hg19 hg19 /genedata/human_genome_GRCh37/**hg19.fa >>> >>> (Spaces are actually tabs!) >>> >>> >>> After all that, I neither have the "Map with BWA for Illumina >>> <https://main.g2.bx.psu.edu/**tool_runner?tool_id=toolshed.** >>> g2.bx.psu.edu/repos/devteam/**bwa_wrappers/bwa_wrapper/1.2.3<https://main.g2.bx.psu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3> >>> **>" >>> >>> in my local Galaxy version, nor do I find the reference genome. >>> If i missed on any required, please tell me, I will answer you as soon >>> as possible. >>> Sincerly Yours >>> Moritz Juchler >>> >>> >>> ______________________________**_____________________________ >>> 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: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> >>> http://galaxyproject.org/**search/mailinglists/<http://galaxyproject.org/search/mailinglists/> >>> >>> >> >
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