Hi Graham, Which revision of Galaxy are you currently using? Currently data managers require at least 9952:a28faa6ac188 on the default branch. When installed from the tool shed, data managers use the shed_tool_data_table_conf.xml file, could you check the contents of that file? Also can you check the paster.log during server start up for any errors, its most likely the case that this changeset https://bitbucket.org/galaxy/galaxy-central/commits/af20b15f7eda (10145:af20b15f7eda) creates a non-compatiible tool data table entry in the main file. Thanks for using Galaxy, Dan On Jul 12, 2013, at 8:14 AM, graham etherington (TSL) wrote:
Hi, I've tried using the Data Manager (Admin > Data > Manage local data (beta)) to install builds for BWA and Samtools on my local Galaxy instance. Previous to using the Data Manager, I used to add the build to tool-data/shared/ucsc/builds.txt, create the .fai indexes (for samtools) from the command line, add them to tool-data/sam_fa_indices.loc and restart Galaxy (obviously doing a similar thing for BWA and adding the build to bwa_index.loc).
I thought I'd try using the Data Manager to add builds for BWA and Samtools. The BWA builds work fine (I can map to the build), but when I try to use SAM-to-BAM I get the error "Sequences are not currently available for the specified build."
Using the Data Manager creates the directory tool-data/n_sylvestris/ which contains the sub-dirs 'seq', 'bwa_index' and 'sam_index'. 'seq' contains a symlink to the n_sylvestris.fa sequence. 'sam_index' and 'bwa_index' both contains the sub-directory 'n_sylvestris', which contains a symlink to the symlink for n_sylvestris.fa in 'seq' along with their respective n_sylvestris.fa.xxx index files.
OK - all goodŠ
In tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/ there are three subdirectories: data_manager_bwa_index_builder, data_manager_sam_fa_index_builder and data_manager_fetch_genome_all_fasta All three directories contain all_fasta.loc, tool_data_table_conf.xml, tool_data_table_conf.xml.sample and (for sam and bam dirs) their pertinent index.loc file.
The data_manager_fetch_genome_all_fasta/all_fasta.loc file contains the path to the fasta symlinks.
The all_fasta.loc files in the sam and bwa data_manager_index_builder directories don't contain any uncommented lines.
The index.loc files in the sam and bwa data_manager_index_builder directories point to: tool-data/n_sylvestris/bwa_index/n_sylvestris/n_sylvestris.fa tool-data/n_sylvestris/sam_index/n_sylvestris/n_sylvestris.fa
As BWA runs fine, it's obviously reading the bwa_index.loc file from the directory: tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_ind ex_builder/fe6508204acc/bwa_index.loc
...but it's not reading the samtools indexes at: tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_sam_fa_ index_builder/926e50397b83/sam_fa_indices.loc
For Galaxy to find the sam indexes, I have to go to the tool-data/sam_fa_indices.loc file and manually insert into it the contents of: tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_sam_fa_ index_builder/926e50397b83/sam_fa_indices.loc
So, I guess my question is: other than inserting the genome builds into builds.txt, should I be doing any other configuration to get Data Manager to write and configure Galaxy to read it's newly created builds. I find it strange that the BWA builds work OK, but the Samtools ones don't.
I've done a few greps for mentions of .loc files in Galaxy and the only difference between the bwa and sam .loc files is that there is a file tool-data/tool_data_table_conf.xml (plus a .sample version) which contains:
<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> <tables> <!-- Location of SAMTools indexes and other files --> <table name="sam_fa_indexes" comment_char="#"> <columns>line_type, value, path</columns> <file path="tool-data/sam_fa_indices.loc" /> </table> </tables>
Could Galaxy be reading this file and ignoring the one in tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/ ??
Best wishes, Graham
Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
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