fix for conda

ngs-fzb · Sep 26, 2018 · 4b90af5 · 4b90af5
1 parent 89e6dcf
commit 4b90af5
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/MANUAL.md b/MANUAL.md
@@ -93,7 +93,7 @@ MTBseq can then be installed with:
 
 Due to license restrictions, even bioconda cannot install the dependency GenomeAnalysisTK 3.8 directly. After installation of MTBseq to fully install the GATK, you must download a licensed copy of the GenomeAnalysisTK 3.8  from the Broad Institute ([GATK Version 3.8](https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-0-ge9d806836)), and call 
 
-`gatk3-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]`
+`gatk-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]`
 
  which will copy GATK into your conda environment.
 

diff --git a/MTBseq b/MTBseq
@@ -163,7 +163,7 @@ warn "<WARN>\t",timer(),"\tFor this execution of MTBseq samtools 1.6 from the MT
 $SAMTOOLS_call="$BIN_dir\/samtools";}
 
 open (my $java_ver, '-|', 'java -version 2>&1') or die "<ERROR>\t",timer(),"\tCould not test java version\n"; my $java_ver_out = <$java_ver>; close $java_ver;
-$java_ver_out =~ qr/openjdk\sversion\s\"(\d+\.\d+)\.\d+_\d+\"/ms;
+$java_ver_out =~ qr/openjdk\sversion\s\"(\d+\.\d+)\.\d+_\S+\"/ms;
 my $java_version = defined $1 ? $1 : 0;
 unless ($java_version == 1.8) {
 die "<ERROR>\t",timer(),"\tNeed exatly java 1.8 for GATK execution. You have java $java_version!\n";}

diff --git a/README.md b/README.md
@@ -21,7 +21,7 @@ After installation of MTBseq to fully install the GATK, you must download a lice
  from the Broad Institute (https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-0-ge9d806836), 
  and call
 ``` 
-gatk3-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]
+gatk-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]
 ```
 , which will copy GATK into your conda environment.