Hi Sarah,

NCBI made some changes and the scripts to obtain all of this data in one go are considered deprecated (for now - a ticket to update the scripts is open here: https://trello.com/c/ehx5Gvr7). You may be able to work out how to adjust them yourself, if familiar with how the data is organized or simply have some programming background and wish to explore it and do some testing. The changes are not expected to be large, just are low priority by necessity for our team at this time.

Another alternative is to rsync what we have available. The " microbes" directory would be the target (as listed in the wiki) - but be warned, this will be large. Also, be sure to add the genomes to the builds.txt file for them to work properly in your local UI, restart, etc.

Meanwhile, the recommended way to set up any microbial genomes not available through rsync or just in general would be the same as for all other genomes - following the instructions in this wiki and ones that link from it:
If you look at the genomes in the rsync area, you will see that we have some microbial data in the general top-level genome pool as well, so organizing the data this way is fine.

Thanks for your patience Sarah,

Galaxy team

On 4/19/13 7:16 AM, Sarah Maman wrote:

I try to set "Get Microbial Data" in my local instance of Galaxy.
So, as explain in /path/to//src/galaxy/galaxy-dist/scripts/microbes/README.txt , step 1 and 2 or OK, binary 'faToNib' is available on our cluster, but step 3 generate empty files :

drwxr-xr-x 4 galaxy wbioinfo 100 18 avril 14:26 ..
-rw-r--r-- 1 galaxy wbioinfo 203 18 avril 14:26 harvest.txt
-rw-r--r-- 1 galaxy wbioinfo  69 18 avril 14:34 ncbi_to_ucsc.txt
-rw-r--r-- 1 galaxy wbioinfo   0 19 avril 15:47 sequence.txt
-rw-r--r-- 1 galaxy wbioinfo   0 19 avril 15:47 seq.loc
drwxr-xr-x 2 galaxy wbioinfo 118 19 avril 15:47 .

Could you please, hel me ?
Thnaks in advance,
Sarah Maman

Jennifer Hillman-Jackson
Galaxy Support and Training