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:
http://wiki.galaxyproject.org/Admin/Data%20Integration#Get_the_data
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,
Jen
Galaxy team
On 4/19/13 7:16 AM, Sarah Maman wrote:
Hello,
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
http://galaxyproject.org