-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathgenomes.config.example
65 lines (54 loc) · 2.62 KB
/
genomes.config.example
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
/*
Clusterflow Genomes
-------------------
Genome paths for clusterflow.
You can use a command-line wizard to automatically search for genome
indices and add them to this file. Just run cf --add_genome
Syntax - @reference ref_type genome_key path species assembly
Reference type can be fasta / bowtie / bowtie2 / star / gtf
Species and assembly are optional and only serve as additional information
Fields are delimited by whitespace, so do not include spaces in species name.
when running cf --list_genomes
-------------------
*/
/***************/
/* Fasta Paths */
/***************/
/* These should be the directories containing the fasta files */
@reference fasta GRCh37 /path/to/genomes/Human/GRCh37/ Human GRCh37
@reference fasta GRCm38 /path/to/genomes/Mouse/GRCm38/ Mouse GRCm38
@reference fasta NCBIM37 /path/to/genomes/Mouse/NCBIM37/ Mouse NCBIM37
/****************/
/* Bowtie Paths */
/****************/
/* These should be the full path including the filename stub */
/* (everything except .[1-4].ebwt) */
@reference bowtie GRCh37 /path/to/genomes/Human/GRCh37/Homo_sapiens.GRCh37 Human GRCh37
@reference bowtie GRCm38 /path/to/genomes/Mouse/GRCm38/Mus_musculus.GRCm38 Mouse GRCm38
@reference bowtie NCBIM37 /path/to/genomes/Mouse/NCBIM37/Mus_musculus.NCBIM37 Mouse NCBIM37
/******************/
/* Bowtie 2 Paths */
/******************/
/* These should be the full path including the filename stub */
/* (everything except .[1-4].bt2) */
@reference bowtie2 GRCh37 /path/to/genomes/Human/GRCh37/Homo_sapiens.GRCh37 Human GRCh37
@reference bowtie2 GRCm38 /path/to/genomes/Mouse/GRCm38/Mus_musculus.GRCm38 Mouse GRCm38
@reference bowtie2 NCBIM37 /path/to/genomes/Mouse/NCBIM37/Mus_musculus.NCBIM37 Mouse NCBIM37
/**************/
/* STAR Paths */
/**************/
@reference star GRCh37 /path/to/genomes/Human/GRCh37/Homo_sapiens.GRCh37 Human GRCh37
@reference star GRCm38 /path/to/genomes/Mouse/GRCm38/Mus_musculus.GRCm38 Mouse GRCm38
@reference star NCBIM37 /path/to/genomes/Mouse/NCBIM37/Mus_musculus.NCBIM37 Mouse NCBIM37
/*************/
/* GTF Paths */
/*************/
/* These should be the full path and filename. */
@reference gtf GRCh37 /path/to/genomes/Human/GRCh37/Homo_sapiens.GRCh37.61.gtf Human GRCh37
@reference gtf GRCm38 /path/to/genomes/Mouse/GRCm38/Mus_musculus.GRCm38.70.gtf Mouse GRCm38
@reference gtf NCBIM37 /path/to/genomes/Mouse/NCBIM37/Mus_musculus.NCBIM37.cleaned.gtf Mouse NCBIM37
/*************/
/* BWA Paths */
/*************/
/* These should be the full path including the filename stub */
@reference bwa GRCh37 /path/to/genomes/Human/GRCh37/GRCh37.fa Human GRCh37