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
data_manager_bwa_index_builder, data_manager_sam_fa_index_builder and
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:

As BWA runs fine, it's obviously reading the bwa_index.loc file from the

...but it's not reading the samtools indexes at:

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

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-->
    <!-- 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" />

Could Galaxy be reading this file and ignoring the one in
tool-data/testtoolshed.g2.bx.psu.edu/repos/blankenberg/  ??

Best wishes,

Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
Tel: +44 (0)1603 450601

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