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 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 *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> Then I tried to follow this guide: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup to get the reference files and 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 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>" 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/