diff --git a/.travis/install_deps.sh b/.travis/install_deps.sh index 36821a8..f2022a9 100755 --- a/.travis/install_deps.sh +++ b/.travis/install_deps.sh @@ -7,7 +7,7 @@ WGET="wget --quiet" MAKE="make --silent -j" UNTAR="tar xf" -SAMTOOLSVER=1.9 +SAMTOOLSVER=1.10 SAMTOOLS=samtools-$SAMTOOLSVER echo "* $SAMTOOLS" $WGET https://github.com/samtools/samtools/releases/download/$SAMTOOLSVER/$SAMTOOLS.tar.bz2 @@ -15,9 +15,11 @@ $UNTAR $SAMTOOLS.tar.bz2 (cd $SAMTOOLS && ./configure --prefix=$HERE/$SAMTOOLS && $MAKE install) PATH=$HERE/$SAMTOOLS/bin:$PATH -$WGET https://raw.githubusercontent.com/tseemann/samclip/master/samclip -chmod +x samclip -mv samclip $HERE/$SAMTOOLS/bin +SAMCLIP=samclip +echo "* $SAMCLIP" +$WGET https://raw.githubusercontent.com/tseemann/$SAMCLIP/master/$SAMCLIP +chmod +x $SAMCLIP +mv $SAMCLIP $HERE/$SAMTOOLS/bin BWAVER=0.7.17 BWA=bwa-$BWAVER @@ -52,8 +54,9 @@ $WGET -O $SKESA/skesa https://ftp.ncbi.nlm.nih.gov/pub/agarwala/skesa/skesa.cent chmod +x $SKESA/skesa PATH=$HERE/$SKESA:$PATH -MEGAHITVER=1.1.3 -MEGAHIT=megahit_v${MEGAHITVER}_LINUX_CPUONLY_x86_64-bin +#https://github.com/voutcn/megahit/releases/download/v1.2.9/MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz +MEGAHITVER=1.2.9 +MEGAHIT=MEGAHIT-${MEGAHITVER}-Linux-x86_64-static MEGAHITTAR=$MEGAHIT.tar.gz echo "* $MEGAHIT" $WGET https://github.com/voutcn/megahit/releases/download/v$MEGAHITVER/$MEGAHITTAR