Merge pull request #22 from cancerit/dev

tests checking output of dependancy needed updating
cancerit · Oct 23, 2014 · 1755046 · 1755046
2 parents 74ebc94 + 22a55b8
commit 1755046
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Showing 5 changed files with 5 additions and 3 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,4 @@
 /LICENCE.TXT
 /README.TXT
 /licence_head.txt
+/perl/perltidy.LOG
diff --git a/perl/MANIFEST b/perl/MANIFEST
@@ -34,6 +34,7 @@ lib/Sanger/CGP/Ascat.pm
 lib/Sanger/CGP/Ascat/Implement.pm
 Makefile.PL
 MANIFEST			This list of files
+perltidy.LOG
 share/ascat/ascat.R
 share/ascat/runASCAT.R
 t/1_pm_compile.t

diff --git a/perl/docs.tar.gz b/perl/docs.tar.gz
diff --git a/perl/t/CN_to_VCF.t b/perl/t/CN_to_VCF.t
@@ -94,8 +94,8 @@ my $EXP_OUT = "##fileformat=VCFv4.1\n".
                 "##SAMPLE=<ID=NORMAL,Description=\"$norm_desc\",Accession=$norm_accession,Platform=$norm_platform,Protocol=$norm_protocol,SampleName=TESTNORM,Source=$norm_source,Study=$norm_study>\n".
                 "##SAMPLE=<ID=TUMOUR,Description=\"$mut_desc\",Accession=$mut_accession,Platform=$mut_platform,Protocol=$mut_protocol,SampleName=TESTMUT,Source=$mut_source,Study=$mut_study>\n".
                 "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOUR\n".
-                "22\t10000009\t.\tN\t<CNV>\t.\t.\tSVTYPE=CNV;END=62896419\t./.:2:1\t./.:3:1\n".
-                "22\t10000024\t.\tN\t<CNV>\t.\t.\tSVTYPE=CNV;END=63111528\t./.:2:1\t./.:5:2\n";
+                "22\t10000009\t.\tN\t<CNV>\t.\t.\tSVTYPE=CNV;END=62896419\tGT:TCN:MCN\t./.:2:1\t./.:3:1\n".
+                "22\t10000024\t.\tN\t<CNV>\t.\t.\tSVTYPE=CNV;END=63111528\tGT:TCN:MCN\t./.:2:1\t./.:5:2\n";
 
 
 subtest 'Good segments file test' => sub{

diff --git a/setup.sh b/setup.sh
@@ -121,7 +121,7 @@ if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
 fi
 (
   set -x
-  bin/cpanm -v --mirror http://cpan.metacpan.org -notest -l $INST_PATH/ --installdeps . < /dev/null
+  bin/cpanm -v --mirror http://cpan.metacpan.org --notest -l $INST_PATH/ --installdeps . < /dev/null
   set +x
 ) >>$INIT_DIR/setup.log 2>&1
 done_message "" "Failed during installation of core dependencies."