including files for easy installing procedures

Author: celiosantosjr

install.sh

@@ -0,0 +1,54 @@
+set -v
+set -e
+
+# This is set in travis
+if [[ x$PYTHON_VERSION == x ]]; then
+    PYTHON_VERSION=3.9
+fi
+
+
+echo "
+# GMSC-Mapper
+AUTHORS: Yiqian Duan, Celio Dias Santos Junior, Luis Pedro Coelho
+"
+
+if ! which conda > /dev/null; then
+    echo "[ Conda not found. Please install miniconda and add 'conda' to the PATH: "
+    echo "    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
+    echo "    sh Miniconda3-latest-Linux-x86_64.sh"
+    exit 1
+fi
+
+eval "$(conda shell.bash hook)"
+
+BASEDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+
+echo "# Creating new environment for GMSC-mapper"
+mkdir -p envs
+
+conda config --env --add channels defaults
+conda config --env --add channels bioconda
+conda config --env --add channels conda-forge
+
+if ! which mamba > /dev/null; then
+    CONDA_INSTALL_CMD=conda
+else
+    echo "# Installing packages with MAMBA"
+    CONDA_INSTALL_CMD=mamba
+fi
+
+${CONDA_INSTALL_CMD} env create \
+          -p $BASEDIR/envs/gmscmapper \
+          -f $BASEDIR/environment.yml
+
+# only activate AFTER install all the packages to get the right environmental variables
+source activate $BASEDIR/envs/gmscmapper
+python3 $BASEDIR/setup.py install
+bash $BASEDIR/tests.sh
+
+echo "############ Installation procedures finished
+****** Thank you for installing GMSC-Mapper ********
+--- Please submit bugreports/comments to
+https://github.com/BigDataBiology/GMSC-mapper/issues"
+

tests.sh

@@ -0,0 +1,24 @@
+set -v
+set -e
+
+echo "# GMSC-Mapper
+AUTHORS: Yiqian Duan, Celio Dias Santos Junior, Luis Pedro Coelho"
+
+echo "Creating mocking databases"
+gmsc-mapper createdb -i examples/target.faa -o examples/ -m diamond
+gmsc-mapper createdb -i examples/target.faa -o examples/ -m mmseqs
+
+echo "Testing basic usage"
+gmsc-mapper -i examples/example.fa --db examples/targetdb.dmnd --habitat examples/ref_habitat.txt --quality examples/ref_quality.txt --taxonomy examples/ref_taxonomy.txt
+gmsc-mapper --aa-genes examples/example.faa --db examples/targetdb.dmnd --habitat examples/ref_habitat.txt --quality examples/ref_quality.txt --taxonomy examples/ref_taxonomy.txt
+gmsc-mapper --nt-genes examples/example.fna --db examples/targetdb.dmnd --habitat examples/ref_habitat.txt --quality examples/ref_quality.txt --taxonomy examples/ref_taxonomy.txt
+
+echo "Testing flags for no alternative results"
+gmsc-mapper -i examples/example.fa --db examples/targetdb.dmnd --habitat examples/ref_habitat.txt --quality examples/ref_quality.txt --taxonomy examples/ref_taxonomy.txt --nohabitat --notaxonomy --noquality
+
+echo "Testing tool flag - MMSeqs"
+gmsc-mapper -i examples/example.fa --db examples/targetdb --habitat examples/ref_habitat.txt --quality examples/ref_quality.txt --taxonomy examples/ref_taxonomy.txt --tool mmseqs
+
+echo "Testing tool flag - Diamond"
+gmsc-mapper -i examples/example.fa --db examples/targetdb --habitat examples/ref_habitat.txt --quality examples/ref_quality.txt --taxonomy examples/ref_taxonomy.txt --tool diamond
+