diff --git a/install_dependencies.sh b/install_dependencies.sh index 6a15f55..66319f5 100755 --- a/install_dependencies.sh +++ b/install_dependencies.sh @@ -1,5 +1,5 @@ #!/bin/bash -# last update: 2019/01/18 +# last update: 2019/02/28 set -e -o pipefail @@ -85,7 +85,8 @@ SRA_DOWNLOAD_URL="https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/srat PORECHOP_DOWNLOAD_URL="https://github.com/rrwick/Porechop.git" FILTLONG_DOWNLOAD_URL="https://github.com/rrwick/Filtlong.git" MINIMAP2_DOWNLOAD_URL="https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2" -CANU_DOWNLOAD_URL="https://github.com/marbl/canu/archive/v${CANU_VERSION}.tar.gz" +CANU_DOWNLOAD_URL="https://github.com/marbl/canu/releases/download/v${CANU_VERSION}/canu-${CANU_VERSION}.Linux-amd64.tar.xz" +#CANU_DOWNLOAD_URL="https://github.com/marbl/canu/archive/v${CANU_VERSION}.tar.gz" FLYE_DOWNLOAD_URL="https://github.com/fenderglass/Flye/archive/${FLYE_VERSION}.tar.gz" WTDBG2_DOWNLOAD_URL="https://github.com/ruanjue/wtdbg2.git" SMARTDENOVO_DOWNLOAD_URL="https://github.com/ruanjue/smartdenovo" @@ -250,7 +251,7 @@ py3_virtualenv_porechop/bin/python3 ./setup.py install deactivate porechop_dir="$build_dir/Porechop/py3_virtualenv_porechop/bin" -# --------------- Porechop ------------------ +# --------------- Filtlong ------------------ cd $build_dir echo "Download Filtlong-v${FILTLONG_VERSION}" git clone $FILTLONG_DOWNLOAD_URL @@ -270,17 +271,29 @@ rm minimap2-${MINIMAP2_VERSION}.tar.bz2 # ------------- Canu ------------------- cd $build_dir echo "Download Canu-v${CANU_VERSION}" -download $CANU_DOWNLOAD_URL "canu-${CANU_VERSION}.tar.gz" -tar -xzf canu-${CANU_VERSION}.tar.gz +download $CANU_DOWNLOAD_URL "canu-${CANU_VERSION}.tar.xz" +tar -xf canu-${CANU_VERSION}.tar.xz canu_dir="$build_dir/canu-${CANU_VERSION}" cd $canu_dir -cd src -make -j 8 canu_dir="$build_dir/canu-${CANU_VERSION}/Linux-amd64/bin" cd $canu_dir ln -s $minimap2_dir/minimap2 . cd $build_dir -rm canu-${CANU_VERSION}.tar.gz +rm canu-${CANU_VERSION}.tar.xz + +# cd $build_dir +# echo "Download Canu-v${CANU_VERSION}" +# download $CANU_DOWNLOAD_URL "canu-${CANU_VERSION}.tar.gz" +# tar -xzf canu-${CANU_VERSION}.tar.gz +# canu_dir="$build_dir/canu-${CANU_VERSION}" +# cd $canu_dir +# cd src +# make -j 8 +# canu_dir="$build_dir/canu-${CANU_VERSION}/Linux-amd64/bin" +# cd $canu_dir +# ln -s $minimap2_dir/minimap2 . +# cd $build_dir +# rm canu-${CANU_VERSION}.tar.gz # ------------- Flye ------------------- cd $build_dir @@ -526,7 +539,7 @@ rm ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz cd "ncbi-blast-${BLAST_VERSION}+" mkdir matrices cd matrices -wget ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/* +wget -nv --no-check-certificate ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/* blast_dir="$build_dir/ncbi-blast-${BLAST_VERSION}+/bin" blast_matrices_dir="$build_dir/ncbi-blast-${BLAST_VERSION}+/matrices" @@ -603,7 +616,7 @@ repeatmasker_dir="$build_dir/RepeatMasker" cd $repeatmasker_dir echo "Download and setup RepBase library" REPBASE_VERSION="20170127" -wget https://github.com/yjx1217/RMRB/raw/master/RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz +wget -nv --no-check-certificate https://github.com/yjx1217/RMRB/raw/master/RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz tar xzf RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz rm RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz cd .. @@ -740,7 +753,7 @@ cd $build_dir echo "Create GATK3 folder for users' manual installation" mkdir GATK3 cd GATK3 -wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/GenomeAnalysisTK.jar +wget -nv --no-check-certificate https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/GenomeAnalysisTK.jar chmod 755 GenomeAnalysisTK.jar gatk_dir="$build_dir/GATK3"