add binary generation framework

.make_binaries.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+
+# Just a script to make various kallisto binaries (works on mac; some adjustments may need to be made for other OS's, but this provides a basic framework)
+
+os="mac"
+
+
+
+# Standard build
+
+rm -rf kallisto
+git clone https://github.com/pachterlab/kallisto
+cd kallisto
+mkdir build
+cd build
+cmake .. -DUSE_HDF5=ON -DUSE_BAM=ON -DBUILD_FUNCTESTING=ON
+make
+version=$(./src/kallisto version|cut -d' ' -f3|tr -d '\n')
+mkdir kallisto
+mv ./src/kallisto ./kallisto/
+cp -R ../test/ ./kallisto/test/
+cp ../README.md ./kallisto/
+cp ../license.txt ./kallisto/
+tar --no-xattrs --exclude='._*' -czvf kallisto_${os}-v${version}.tar.gz kallisto
+cp kallisto_${os}-v${version}.tar.gz ../../
+cd ../../
+
+# Long k-mer build
+
+rm -rf kallisto
+git clone https://github.com/pachterlab/kallisto
+cd kallisto
+mkdir build
+cd build
+cmake .. -DUSE_HDF5=ON -DUSE_BAM=ON -DMAX_KMER_SIZE=64
+make
+version=$(./src/kallisto version|cut -d' ' -f3|tr -d '\n')
+cp src/kallisto ../../kallisto_${os}-v${version}_kmer64
+cd ../../
+
+# Disable opt build
+
+rm -rf kallisto
+git clone https://github.com/pachterlab/kallisto
+cd kallisto
+mkdir build
+cd build
+cmake .. -DUSE_HDF5=ON -DUSE_BAM=ON -DBUILD_FUNCTESTING=ON -DENABLE_AVX2=OFF -DCOMPILATION_ARCH=OFF
+make
+version=$(./src/kallisto version|cut -d' ' -f3|tr -d '\n')
+mv src/kallisto ../../kallisto_${os}-v${version}_optoff
+cd ../../
+
+
+
+# Disable opt build but have long k-mer
+
+rm -rf kallisto
+git clone https://github.com/pachterlab/kallisto
+cd kallisto
+mkdir build
+cd build
+cmake .. -DUSE_HDF5=ON -DUSE_BAM=ON -DBUILD_FUNCTESTING=ON -DENABLE_AVX2=OFF -DCOMPILATION_ARCH=OFF -DMAX_KMER_SIZE=64
+make
+version=$(./src/kallisto version|cut -d' ' -f3|tr -d '\n')
+mv src/kallisto ../../kallisto_${os}-v${version}_optoff_k64
+cd ../../
+
+