Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate README @ 1:3a2e0f376f26 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
1 installation instructions cgatools:
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
2
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
3
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
4 reference data
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
5 ------------------------
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
6 Get .crr files from CG ftp site:
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
7 - ftp://ftp.completegenomics.com/ReferenceFiles/build36.crr
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
8 - ftp://ftp.completegenomics.com/ReferenceFiles/build37.crr
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
9
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
10 Get calibration root file:
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
11 - ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
12
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
13 Get other reference file from CG ftp site:
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
14 - ftp://ftp.completegenomics.com/AnnotationFiles/gene36.tsv.gz
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
15 - ftp://ftp.completegenomics.com/AnnotationFiles/rmsk36.tsv.gz
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
16 - ftp://ftp.completegenomics.com/AnnotationFiles/segdup36.tsv.gz
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
17 - ftp://ftp.completegenomics.com/AnnotationFiles/gene37.tsv.gz
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
18 - ftp://ftp.completegenomics.com/AnnotationFiles/rmsk37.tsv.gz
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
19 - ftp://ftp.completegenomics.com/AnnotationFiles/segdup37.tsv.gz
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
20
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
21
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
22 And unzip them to desired location.
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
23
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
24
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
25 Adjust cgatools.loc file (included in repository) to reflect the locations of the reference files you dowloaded.
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
26
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
27
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
28 datatypes
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
29 ------------------------
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
30
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
31 <!-- Start Complete Genomics Datatypes -->
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
32 <datatype extension="cg_var" type="galaxy.datatypes.completegenomics:CG_Var" display_in_upload="true" />
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
33 <datatype extension="cg_mastervar" type="galaxy.datatypes.completegenomics:CG_MasterVar" display_in_upload="true" />
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
34 <datatype extension="cg_gene" type="galaxy.datatypes.completegenomics:CG_Gene" display_in_upload="true" />
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
35 <!-- End Complete Genomics Datatypes -->
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
36
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
37
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
38