Changes between Version 3 and Version 4 of cypress/WGSA


Ignore:
Timestamp:
Jul 15, 2020 12:07:48 AM (2 years ago)
Author:
fuji
Comment:

Legend:

Unmodified
Added
Removed
Modified
  • cypress/WGSA

    v3 v4  
    11[[PageOutline]]
    22= Installing and Setup WGSA in a local directory on Cypress =
     3This instruction is based on [https://sites.google.com/site/jpopgen/wgsa/setting-up-wgsa-linux this] page and adapted for Cypress.
     4
    35Decide a folder dedicated for the pipeline, for example '/lustre/project/group/WGSA'.
    46
     
    1719
    1820{{{
    19 mkdir $WGSA_DIR/annovar
     21mkdir $WGSA_DIR/annovar2019Oct24
    2022}}}
    2123
    2224
    2325Download the ANNOVAR main package from [http://download.openbioinformatics.org/annovar_download_form.php here].
    24 The package comes as annovar.latest.tar.gz, save it to $WGSA_DIR/annovar. Unzip it.
     26The package comes as annovar.latest.tar.gz, save it to $WGSA_DIR/annovar2019Oct24. Unzip it.
    2527
    2628
    2729{{{
    28 cd $WGSA_DIR/annovar
     30cd $WGSA_DIR/annovar2019Oct24
    2931tar -zxvf annovar.latest.tar.gz
    3032}}}
    3133
    32 Download !RefSeq and !Ensembl gene models for ANNOVAR:
     34Download !RefSeq and Ensembl gene models for ANNOVAR:
    3335
    3436{{{
    35 cd $WGSA_DIR/annovar/annovar
     37cd $WGSA_DIR/annovar2019Oct24/annovar
    3638perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/
    3739perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar ensGene humandb/
     
    5759
    5860{{{
    59 idev
     61idev -c 1 -t 4
    6062}}}
    61 
     63It will take more than one hour.
    6264See [https://wiki.hpc.tulane.edu/trac/wiki/Workshops/IntroToHpc2015/using#SubmittingInteractiveJobs here] for more about 'idev'.
    6365