3.4 years ago by
United States
Furthermore, This is absolute position for my human bowtie2_index(path=xxxx@gmail.com/galaxy/tool-data/hg19/bowtie2_index) .Open each biwtie2_indices.loc, we can see as follow:
# bowtie2_indices.loc.sample
# This is a *.loc.sample file distributed with Galaxy that enables tools
# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
# First create these data files and save them in your own data directory structure.
# Then, create a bowtie_indices.loc file to use those indexes with tools.
# Copy this file, save it with the same name (minus the .sample),
# follow the format examples, and store the result in this directory.
# The file should include an one line entry for each index set.
# The path points to the "basename" for the set, not a specific file.
# It has four text columns seperated by TABS.
#
# <unique_build_id> <dbkey> <display_name> <file_base_path>
#
# So, for example, if you had hg18 indexes stored in:
#
# /depot/data2/galaxy/hg19/bowtie2/
#
# containing hg19 genome and hg19.*.bt2 files, such as:
# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
#
# then the bowtie2_indices.loc entry could look like this:
#
#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon
#
#More examples:
#
#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10
#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3
#
#
I wonder that the path like (hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon) or (/depot/data2/galaxy/hg19/bowtie2/) is not absolute position for genome index. Why bowtie2 software can work, while tophat2 can not. I also change these paths as absolute positions in bowtie2_indices.loc in tophat2 files. It is still does not work.Would you like to help me and give me some detailed steps, according to my current file position. Thank you very much in advance
Many thanks Nicholas. I think I'd followed the same steps as you - using the data manager to generate the bowtie2 index (for use in tophat2). But couldn't fathom why there was no reference genome available in the drop down.
Followed your workaround - now it's working.
much appreciated.
Simon (GUDMAP www.gudmap.org)
I also met this problem and right now can not solve it . I am confused by your instruction. you mean :copy bowtie2_indices.loc from (galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/bowtie2_indices.loc) to bowtie2_indices.loc (/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/5c5517d2a9e9/bowtie2_indices.loc).Would you like to introduce this to me. Thank you very much!
Assuming you have a file /galaxy in the top directory and that you've generated a bowtie2 index using the data_manager tools (so you should be able to see a reference genome when you look at the bowtie2 tool in galaxy) just do as one line:
tail -n 2 /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/bowtie2_indices.loc >> /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/5c5517d2a9e9/bowtie2_indices.loc
which will take the final lines specifying the location of the index in bowtie2 index file and add them to the tophat2 index file.
HI, Would you like to help me solve this problem? thank you !