-
Notifications
You must be signed in to change notification settings - Fork 0
/
README
76 lines (50 loc) · 2.67 KB
/
README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
NOTE - Please do not touch the targets.json file. gkno relies on it
for proper resource management. Thanks. :)
----------------------------------------------
-- Looking for this genome's resource data? --
----------------------------------------------
From the launcher's root directory, typing:
./gkno add-resource
will display a list of all genomes that gkno is hosting and can fetch for you.
If you see the organism you're looking for, typing:
./gkno add-resource <organism>
will download its current genome build, or release. That release's files will be
stored under the organism's directory:
(i.e. .../gkno_launcher/resources/homo_sapiens/build_37).
In addition, a symlink (shortcut) named "current" will be created in the
organism's directory that points to the current release.
Later, in addition to updating gkno itself, typing:
./gkno update
will show a list of all organisms with new 'current' releases. Typing:
./gkno update-resource <organism>
will fetch its into the organism's directory, and move the "current" symlink to
point to the new release data. You may also add the new release without
changing the "current" shortcut (see below on adding particular releases).
Most organisms have named "aliases" that you may use when adding or removing
resources. For example, typing:
./gkno add-resource human
./gkno remove-resource mouse
./gkno update-resource c.elegans
would have the same effect same as typing:
./gkno add-resource homo_sapiens
./gkno remove-resource mus_musculus
./gkno update-resource caenorhabditis_elegans
but *much* easier to type. :)
------------------------------------------------------
-- Want to add a particular (older) genome release? --
------------------------------------------------------
As new genome versions are released, you may find that the most current one is
not the one you want to work with. If we host an older release, it's easy to
fetch. From the launcher's root directory, typing:
./gkno add-resource <organism> --release
will display a list all available releases for that genome. Once you see the
release you want, typing (for example):
./gkno add-resource human --release build_36.3
will store that release of the genome in a subdirectory called build_36.3
( .../gkno_launcher/resources/homo_sapiens/build_36.3/ ).
gkno can handle multiple releases for a particular genome, so feel free to add
as many or as few releases as you need. Just be sure to specify the correct
resource path when you run a pipe or tool command.
This approach also works for grabbing a newer release without changing your
organism's "current" symlink.
----------------------------------------