Giter Club home page Giter Club logo

rhshah / impact-pipeline Goto Github PK

View Code? Open in Web Editor NEW
55.0 10.0 9.0 2.46 MB

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

Home Page: http://impact-pipeline.readthedocs.org/en/latest/index.html

License: Apache License 2.0

Perl 63.12% Python 5.80% R 1.80% Shell 0.25% Makefile 0.66% Batchfile 0.65% CSS 2.14% JavaScript 8.95% HTML 16.64%
ngs cancer-genomics precision-medicine cancer-variants illumina-sequencing mskimpact msk-impact

impact-pipeline's Issues

Can't open /home/xxx/IMPACT_central.log (No such file or directory)

When I run this script that returned an exception to me.

Can't open /home/xxx/IMPACT_central.log (No such file or directory) at /IMPACT-Pipeline-1.0.1/sofeware/localperl/lib/site_perl/5.20.2/Log/Log4perl/Appender/File.pm line 151.
BEGIN failed--compilation aborted at /data/PRO/pro_cancer/pipeline/IMPACT-Pipeline-1.0.1/bin/RunIlluminaProcess.pl line 111.

As you know, a part of Linux systems set $HOME not equal '/home/yourname/'. I found the bug in the below script.

IMPACT-Pipeline/custom_perl_module/MSKCC_DMP_Logger.pm

Line 156 in 7b34bff

my $uName = `whoami`;

fix below:

my $uName = `echo \$HOME`;

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.