Hi,

We have just installed a local Galaxy instance on a workstation and I am having issues getting references to show up for my samtools section.  I have setup many.loc files correctly for my other tools and I am able to see and use them in Galaxy.

In the paster.log I see the following:

galaxy.tools.data WARNING 2013-07-10 17:05:06,034 Line 30 in tool data table 'sam_fa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):

index     hg19      /mnt/data3/Reference/human/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa

galaxy.tools.data WARNING 2013-07-10 17:05:06,034 Line 31 in tool data table 'sam_fa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):

index     mm10   /mnt/data3/Reference/mouse/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa

galaxy.tools.data DEBUG 2013-07-10 17:05:06,034 Loaded tool data table 'sam_fa_indexes'

I know for a fact that when I first created this file I had a space (not a TAB) in between index and the  build.  After restarting the Galaxy service several times and double checking our loc files I noticed the error and replace the space with a TAB.

Using vi (with :set list) we see that there are TABs in between the fields. 

#index^Ihg18^I/depot/data2/galaxy/sam/hg18.fa$

#index^Ihg19^I/depot/data2/galaxy/sam/hg19.fa$

index^Ihg19^I/mnt/data3/Reference/human/Homo_sapiens/UCSC/hg19/Sequence/sam/hg19.fa$

index^Imm10^I/mnt/data3/Reference/mouse/Mus_musculus/UCSC/mm10/Sequence/sam/mm10.fa$

Even with the correct file, I still get the same error in the paster.log.  Does this get saved in the database?  How do I resolve this?

Thanks for the help!

Ryan