gatk change for bioconda (#30)

gatk is now gatk3

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 
 
-`gatk-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]`
+`gatk3-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]`
 
  which will copy GATK into your conda environment.
 

MTBseq

@@ -112,7 +112,7 @@ GetOptions('step:s'        =>    \$step,
           );
 
 #set tool calls
-my $GATK_call       =   "gatk";
+my $GATK_call       =   "gatk3";
 my $PICARD_call     =   "picard";
 my $SAMTOOLS_call     =   "samtools";
 my $BWA_call     =   "bwa";
@@ -132,7 +132,7 @@ for my $module (qw(
         print "<INFO>\t",timer(),"\tFound perl module: $module\n";}}
 
 # check for neccessary programs
-for my $executable (qw(bwa samtools gatk picard)) {
+for my $executable (qw(bwa samtools gatk3 picard)) {
    if (my $canrun = can_run($executable)){
       print "<INFO>\t",timer(),"\tFound $executable in your PATH!\n";}
    elsif ($canrun = can_run("$BIN_dir\/$executable")){
@@ -141,7 +141,7 @@ for my $executable (qw(bwa samtools gatk picard)) {
       $SAMTOOLS_call="$BIN_dir\/$executable";}
       elsif ($executable=~"bwa"){
       $BWA_call="$BIN_dir\/$executable";}}
-   elsif ($executable=~"gatk"){
+   elsif ($executable=~"gatk3"){
       if (-f "$BIN_dir\/GenomeAnalysisTK.jar"){
       $GATK_call="java -jar $BIN_dir\/GenomeAnalysisTK.jar";
       print "<INFO>\t",timer(),"\tFound $executable in the MTBseq $BIN_dir folder!\n";}
@@ -154,7 +154,7 @@ for my $executable (qw(bwa samtools gatk picard)) {
    else {die "<ERROR>\t",timer(),"\t$executable is not installed or not in your PATH!\n\n";}}
 
 #check version
-open (my $sam_ver, '-|', '$SAMTOOLS_call --version 2>&1') or die "<ERROR>\t",timer(),"\tCould not test samtools version\n"; my $sam_ver_out = <$sam_ver>; close $sam_ver;
+open (my $sam_ver, '-|', "$SAMTOOLS_call --version 2>&1") or die "<ERROR>\t",timer(),"\tCould not test samtools version\n"; my $sam_ver_out = <$sam_ver>; close $sam_ver;
 $sam_ver_out =~ qr/samtools\s(\d+\.\d+)/ms;
 my $sam_version = defined $1 ? $1 : 0;
 if ($sam_version < 1.6) {

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
 ``` 
-gatk-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]
+gatk3-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]
 ```
 , which will copy GATK into your conda environment.