annotate test-data/lastz_seqs.loc @ 7:94a50db37d1a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author iuc
date Sun, 16 Apr 2023 08:31:43 +0000
parents 5c77d4091880
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
2 #to use a directory of 2bit genome files for use with Lastz. You will
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
3 #need to supply these files and then create a lastz_seqs.loc file
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
4 #similar to this one (store it in this directory) that points to
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
5 #the directories in which those files are stored. The lastz_seqs.loc
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
6 #file has this format (white space characters are TAB characters):
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
7 #
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
8 #<unique_build_id> <display_name> <file_path>
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
9 #
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
10 #So, for example, if your lastz_seqs.loc began like this:
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
11 #
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
12 #hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
13 #hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
14 #mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
15 #
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
16 #then your /depot/data2/galaxy/twobit/ directory
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
17 #would need to contain the following 2bit files:
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
18 #
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
22 #
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
23 #Your lastz_seqs.loc file should include an entry per line for
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
24 #each file you have stored that you want to be available. Note that
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
25 #your files should all have the extension '2bit'.
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
26 #
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
27 #Note that for backwards compatibility with workflows, the unique ID of
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
28 #an entry must be the path that was in the original loc file, because that
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
29 #is the value stored in the workflow for that parameter.
5c77d4091880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
iuc
parents:
diff changeset
30 #