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 goodÅ 
> 
> 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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