Re: [galaxy-dev] Fwd: Map with BWA results in correpted SAM file
Through toolshed. On 14 August 2013 12:50, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Moritz, do you installed bwa through the toolshed or manually? Cheers, Bjoern Hey Folks, Is there really nobody that can help Geert and me? Thats quite important to me right now. This is obviously not something specific to me, as Geert has the exact same error. I meanwhile tried to replace the id with 1 but it still doesnt work. Best Moritz __ Von: galaxy-dev-boun...@lists.bx.psu.eduIm Auftrag vonGeert Vandeweyer Gesendet: Donnerstag, 8. August 2013 17:18:59 (UTC+01:00) Amsterdam, Berlin, Bern, Rom, Stockholm, Wien An: galaxy-dev@lists.bx.psu.edu Betreff: Re: [galaxy-dev] Map with BWA results in correpted SAM file to add on this : we have similar issues (sam-to-bam conversion fails with similar errors). it seems to be related to the BWA output getting messed up, with (part of) columns missing or duplicated on some lines. I have not found a systematic pattern in the errors, they seem to happen rather random. On 08/08/2013 05:06 PM, Moritz Juchler wrote: Dear Galaxy Community, I have a local instance and installed 0.5.9-r16 BWA and the toolshed wrapper. The mapping is successful. I then use the Filter Sam Tool on the sam file from the alignment, but it spits out this error: Dataset 26: Filter SAM on data 24 Tool execution generated the following error message: Traceback (most recent call last): File /home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py, line 148, in module if __name__ == __main__: main() File /home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py, line 137, in main flags = int( fields[flag_col] ) ValueError: invalid literal for int() with base 10: 'RG:Z:lane712s006433' I have the same workflow online and did the exact same steps on the same fastq files. Is there anything I am missing? Is there any information I can provide to answer this question? Best Moritz ___ 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.bemailto:geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ 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/ ___ 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/
[galaxy-dev] Map with BWA results in correpted SAM file
Dear Galaxy Community, I have a local instance and installed 0.5.9-r16 BWA and the toolshed wrapper. The mapping is successful. I then use the Filter Sam Tool on the sam file from the alignment, but it spits out this error: *Dataset 26: Filter SAM on data 24* Tool execution generated the following error message: Traceback (most recent call last): File /home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py, line 148, in module if __name__ == __main__: main() File /home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py, line 137, in main flags = int( fields[flag_col] ) ValueError: invalid literal for int() with base 10: 'RG:Z:lane712s006433' I have the same workflow online and did the exact same steps on the same fastq files. Is there anything I am missing? Is there any information I can provide to answer this question? Best Moritz ___ 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/
[galaxy-dev] Local: BWA 0.5.9. SA Coordinate/Segmentation fault
Hey, 1 I installed Galaxy locally. 2 I also have BWA installed and then used the 3 shed repository to get the bwa wrapper. 4 I have the reference genome now I'm stuck with the calculate SA coordinate. Segmenation fault. Google tells me that it could be a problem with -space (I have 4GB left) -the version I use. (I use 0.5.9 and did a succesful alignment with 0.7.5a, but the tool shed says 0.5.9, hence *could I just change to the current version* (without Galaxy knowing it), with which I did a succesful alignment?) Best Moritz ___ 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/
[galaxy-dev] BWA missing index on reference genome
Hey, 1 I installed Galaxy locally. 2 I also have BWA installed and then used the 3 shed repository to get the bwa wrapper. 4 I have the reference genome: -rw-r--r-- 1 trr users 10509 2013-07-25 11:31 human_g1k_v37.dict -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta -rw-r--r-- 1 trr users 6597 2013-07-25 19:41 human_g1k_v37.fasta.amb -rw-r--r-- 1 trr users 6844 2013-07-25 19:41 human_g1k_v37.fasta.ann -rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt -rw-r--r-- 1 trr users 2746 2013-07-25 11:32 human_g1k_v37.fasta.fai -rw-r--r-- 1 trr users 775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac -rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa 5 and I changed the bwa_index and bw_index_color.loc to the path /genedata/human_genome_GRCh37/hg19.fa 6 This is my *$PATH* trr@portalmoritz:~ echo $PATH /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19 Is there anything I am missing? I would be glad about some help. Best Moritz ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] BWA missing index on reference genome
I solved it so far :) Thanks for your help. On 26 July 2013 16:15, Jennifer Jackson j...@bx.psu.edu wrote: Hi Moritz, Pls see below On Jul 26, 2013, at 6:37 AM, Moritz Juchler juch...@stud.uni-heidelberg.de wrote: Hey, 1 I installed Galaxy locally. 2 I also have BWA installed and then used the 3 shed repository to get the bwa wrapper. 4 I have the reference genome: -rw-r--r-- 1 trr users 10509 2013-07-25 11:31 human_g1k_v37.dict -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta -rw-r--r-- 1 trr users 6597 2013-07-25 19:41 human_g1k_v37.fasta.amb -rw-r--r-- 1 trr users 6844 2013-07-25 19:41 human_g1k_v37.fasta.ann -rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt -rw-r--r-- 1 trr users 2746 2013-07-25 11:32 human_g1k_v37.fasta.fai -rw-r--r-- 1 trr users 775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac -rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa 5 and I changed the bwa_index and bw_index_color.loc to the path /genedata/human_genome_GRCh37/hg19.fa This is the problem - the path must point to the full name of the fasta file. In your case human_g1kv_v37.fasta. Using the name without the fasta as the base name in other fields as the unique dbkey is a good practice. Hopefully this helps, Jen Galaxy team 6 This is my *$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 Is there anything I am missing? I would be glad about some help. Best Moritz ___ 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/ Jennifer Hillman-Jackson Galaxy Support Training http://galaxyproject.org ___ 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/
Re: [galaxy-dev] BWA missing index on reference genome
Hey, now I'm stuck with the calculate SA coordinate. Segmenation fault. Google tells me that it could be a problem with -space (I have 4GB left) -the version I use. (I use 0.5.9 and did a succesful alignment with 0.7.5a, but the tool shed says 0.5.9, hence could I just change to the current version, with which I did a succesful alignment?) Best Moritz On 26 July 2013 16:15, Jennifer Jackson j...@bx.psu.edu wrote: Hi Moritz, Pls see below On Jul 26, 2013, at 6:37 AM, Moritz Juchler juch...@stud.uni-heidelberg.de wrote: Hey, 1 I installed Galaxy locally. 2 I also have BWA installed and then used the 3 shed repository to get the bwa wrapper. 4 I have the reference genome: -rw-r--r-- 1 trr users 10509 2013-07-25 11:31 human_g1k_v37.dict -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta -rw-r--r-- 1 trr users 6597 2013-07-25 19:41 human_g1k_v37.fasta.amb -rw-r--r-- 1 trr users 6844 2013-07-25 19:41 human_g1k_v37.fasta.ann -rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt -rw-r--r-- 1 trr users 2746 2013-07-25 11:32 human_g1k_v37.fasta.fai -rw-r--r-- 1 trr users 775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac -rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa 5 and I changed the bwa_index and bw_index_color.loc to the path /genedata/human_genome_GRCh37/hg19.fa This is the problem - the path must point to the full name of the fasta file. In your case human_g1kv_v37.fasta. Using the name without the fasta as the base name in other fields as the unique dbkey is a good practice. Hopefully this helps, Jen Galaxy team 6 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 Is there anything I am missing? I would be glad about some help. Best Moritz ___ 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/ Jennifer Hillman-Jackson Galaxy Support Training http://galaxyproject.org ___ 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/
Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome
1. Thanks, I'll try this out, after you reavealed me which version I should use :) 2. Originally I had this workflow to start with https://main.g2.bx.psu.edu/u/mj--/w/ngs , but I at the sam-to-bam conversion I get the sequences are not currently available for specified build error when using locally cached and I can't figure out how to use the reference file hg19.fa without actually uploading it to Galaxy, because I do not have enough space on the filesystem where the Galaxy distribution is placed ( /home). The genedata are all on /genedata. So my question here is: How to use the hg19.fa file placed on another filesystem then the galaxydist? 3. Thus I searched the web and found this workaround: https://main.g2.bx.psu.edu/u/mj--/w/sample-workflow-whole-exome-sequencing which runs fine ONLINE AT USE GALAXY but produces this error in my local instance Dataset generation errors *Dataset 18: Filter SAM on data 7* Tool execution generated the following error message: Traceback (most recent call last): File /home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py, line 148, in module if __name__ == __main__: main() File /home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py, line 137, in main flags = int( fields[flag_col] ) IndexError: list index out of range So here is my 3rd question: How to solve this error? I didnt find anything online. Best Moritz On 22 July 2013 16:54, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Jul 22, 2013 at 10:40 AM, Moritz Juchler juch...@stud.uni-heidelberg.de wrote: Hey, now I am having a new problem: Convert SAM to BAM Tool execution generated the following error message: [samopen] SAM header is present: 93 sequences. Parse error at line 106: sequence and quality are inconsistent /bin/sh: line 1: 27934 Aborted samtools view -bS /home/trr/galaxy-dist/database/files/000/dataset_17.dat /tmp/tmp-sam_to_bam_converter-ut5Tag/unsorted.bam That's bad. The tool produced the following additional output: [bam_header_read] EOF marker is absent. The input is probably truncated. (should I make a new post out of this?) Which version of samtools? There is a bug in the currently release where that warning is a false alarm: https://github.com/samtools/samtools/issues/18 Peter ___ 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/
Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome
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.dewrote: 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%**20Tutorialhttp://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%20Galaxyhttp://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%20Setuphttp://wiki.galaxyproject.org/Admin/NGS%20Local%20Setupto get the reference files and http://wiki.galaxyproject.org/**Admin/Config/Tool%**20Dependencieshttp://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies . This is my _$PATH_ trr@portalmoritz:~ echo $PATH /home/trr/bin:/usr/local/bin:/**usr/bin:/bin:/usr/bin/X11:/** usr/X11R6/bin:/usr/games:/**home/trr/bpipe-0.9.8/bin:/** home/trr/bwa-0.7.5a:/home/trr/**samtools-0.1.19 _In the universe_wsgi.ini I changed:_ tool_dependency_dir = /home/trr/galaxy-dist/tool_**dependency_dir debug = False use_interactive = True library_import_dir = /genedata/ allow_library_path_paste = True admin_users = ... This is my _tool_dependency_dir:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa ls -l total 4 drwxr-xr-x 3 trr users 4096 2013-07-16 14:28 0.7.4 lrwxrwxrwx 1 trr users6 2013-07-16 14:17 default - 0.7.4/ This is the_version folder of bwa:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4 ls -l total 8 drwxr-xr-x 2 trr users 4096 2013-07-16 14:18 bin -rw-r--r-- 1 trr users 47 2013-07-16 14:22 env.sh This is the _content of env.sh:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4 cat env.sh PATH=/home/trr/bwa-0.7.5a/:$**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
Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome
Hey, now I am having a new problem: *Convert SAM to BAM *Tool execution generated the following error message: [samopen] SAM header is present: 93 sequences. Parse error at line 106: sequence and quality are inconsistent /bin/sh: line 1: 27934 Aborted samtools view -bS /home/trr/galaxy-dist/database/files/000/dataset_17.dat /tmp/tmp-sam_to_bam_converter-ut5Tag/unsorted.bam The tool produced the following additional output: [bam_header_read] EOF marker is absent. The input is probably truncated. (should I make a new post out of this?) The step I did before was: 7: *Map* with BWA for Illumina on data 5 and data 3: mapped reads ~21,000 lines, 94 comments format: sam, database: hg19 BWA Version: 0.7.5a-r405 BWA run on paired-end data That one seems to work correctly. Any help appreciated :) Best Moritz On 22 July 2013 11:20, Moritz Juchler juch...@stud.uni-heidelberg.dewrote: 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.dewrote: 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%**20Tutorialhttp://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%20Galaxyhttp://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%20Setuphttp://wiki.galaxyproject.org/Admin/NGS%20Local%20Setupto get the reference files and http://wiki.galaxyproject.org/**Admin/Config/Tool%**20Dependencieshttp://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 users6 2013-07-16 14:17 default - 0.7.4/ This is the_version
Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome
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%20Shedhttp://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%**20Tutorialhttp://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%20Galaxyhttp://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%20Setuphttp://wiki.galaxyproject.org/Admin/NGS%20Local%20Setupto get the reference files and http://wiki.galaxyproject.org/**Admin/Config/Tool%**20Dependencieshttp://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies . This is my _$PATH_ trr@portalmoritz:~ echo $PATH /home/trr/bin:/usr/local/bin:/**usr/bin:/bin:/usr/bin/X11:/** usr/X11R6/bin:/usr/games:/**home/trr/bpipe-0.9.8/bin:/** home/trr/bwa-0.7.5a:/home/trr/**samtools-0.1.19 _In the universe_wsgi.ini I changed:_ tool_dependency_dir = /home/trr/galaxy-dist/tool_**dependency_dir debug = False use_interactive = True library_import_dir = /genedata/ allow_library_path_paste = True admin_users = ... This is my _tool_dependency_dir:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa ls -l total 4 drwxr-xr-x 3 trr users 4096 2013-07-16 14:28 0.7.4 lrwxrwxrwx 1 trr users6 2013-07-16 14:17 default - 0.7.4/ This is the_version folder of bwa:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4 ls -l total 8 drwxr-xr-x 2 trr users 4096 2013-07-16 14:18 bin -rw-r--r-- 1 trr users 47 2013-07-16 14:22 env.sh This is the _content of env.sh:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4 cat env.sh PATH=/home/trr/bwa-0.7.5a/:$**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_mappinghttps://bitbucket.org/galaxy
[galaxy-dev] BWA Illumina Mapping / BWA Reference Genome
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 $PATH /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19 *In the universe_wsgi.ini I changed:* tool_dependency_dir = /home/trr/galaxy-dist/tool_dependency_dir debug = False use_interactive = True library_import_dir = /genedata/ allow_library_path_paste = True admin_users = ... This is my *tool_dependency_dir:* trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa ls -l total 4 drwxr-xr-x 3 trr users 4096 2013-07-16 14:28 0.7.4 lrwxrwxrwx 1 trr users6 2013-07-16 14:17 default - 0.7.4/ This is the* version folder of bwa:* trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa/0.7.4 ls -l total 8 drwxr-xr-x 2 trr users 4096 2013-07-16 14:18 bin -rw-r--r-- 1 trr users 47 2013-07-16 14:22 env.sh This is the *content of env.sh:* trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa/0.7.4 cat env.sh PATH=/home/trr/bwa-0.7.5a/:$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 hg19hg19hg19/genedata/human_genome_GRCh37/hg19.fa (Spaces are actually tabs!) After all that, I neither have the Map with BWA for Illuminahttps://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/
