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removing link rot in setup.sh #156

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10 changes: 5 additions & 5 deletions setup.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.3.2/htslib
SOURCE_BIOBDHTS="https://github.com/Ensembl/Bio-HTS/archive/2.3.tar.gz"

# for Bio::DB::BigWig
SOURCE_KENTSRC="ftp://ftp.sanger.ac.uk/pub/cancer/legacy-dependancies/jksrc.v334.zip"
SOURCE_BIGFILE="http://www.cpan.org/authors/id/L/LD/LDS/Bio-BigFile-1.07.tar.gz"
SOURCE_KENTSRC="https://ftp.sanger.ac.uk/pub/cancer/legacy-dependancies/jksrc.v334.zip"
SOURCE_BIGFILE="https://www.cpan.org/authors/id/L/LD/LDS/Bio-BigFile-1.07.tar.gz"

# for biobambam
SOURCE_BBB_BIN_DIST="https://github.com/gt1/biobambam2/releases/download/2.0.54-release-20160802163650/biobambam2-2.0.54-release-20160802163650-x86_64-etch-linux-gnu.tar.gz"
Expand Down Expand Up @@ -110,7 +110,7 @@ if [ -e $SETUP_DIR/basePerlDeps.success ]; then
else
perlmods=( "ExtUtils::CBuilder" "Module::Build~0.42" "File::ShareDir" "File::ShareDir::Install" "Const::Fast" "File::Which" "LWP::UserAgent" "Bio::Root::[email protected]")
for i in "${perlmods[@]}" ; do
$CPANM --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH $i
$CPANM --no-interactive --notest --mirror https://cpan.metacpan.org -l $INST_PATH $i
done
touch $SETUP_DIR/basePerlDeps.success
fi
Expand Down Expand Up @@ -297,12 +297,12 @@ if [ -e $SETUP_DIR/PCAP_perlPrereq.success ]; then
echo "PCAP_perlPrereq previously installed ...";
else
echo
$CPANM --no-interactive --notest --mirror http://cpan.metacpan.org --notest -l $INST_PATH --installdeps .
$CPANM --no-interactive --notest --mirror https://cpan.metacpan.org --notest -l $INST_PATH --installdeps .
touch $SETUP_DIR/PCAP_perlPrereq.success
fi

echo -n "Installing PCAP ..."
$CPANM -v --no-interactive --mirror http://cpan.metacpan.org -l $INST_PATH .
$CPANM -v --no-interactive --mirror https://cpan.metacpan.org -l $INST_PATH .
echo

# cleanup all junk
Expand Down