Update build.sh

bioconda · Oct 11, 2024 · d601431 · d601431
1 parent 6deb803
commit d601431
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/recipes/earlgrey/build.sh b/recipes/earlgrey/build.sh
@@ -27,9 +27,10 @@ cd ../ && rm -rf SA-SSR/
 # Fixes to earlGrey executable
 sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGrey  #remove check that conda environment has a specific name
 sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGreyLibConstruct  #remove check that conda environment has a specific name
+sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGreyearlGreyAnnotationOnly  #remove check that conda environment has a specific name
 
 # Fixes sed command for executables so that it works on both linux and macos
-sed -i.bak "s|sed -i |sed -i.bak |g" ${PACKAGE_HOME}/earlGrey ${PACKAGE_HOME}/earlGreyLibConstruct ${SCRIPT_DIR}/rcMergeRepeat* ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
+sed -i.bak "s|sed -i |sed -i.bak |g" ${PACKAGE_HOME}/earlGrey ${PACKAGE_HOME}/earlGreyLibConstruct ${PACKAGE_HOME}/earlGreyearlGreyAnnotationOnly ${SCRIPT_DIR}/rcMergeRepeat* ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
 
 
 # Remove -pa from RepeatClassifier
@@ -44,6 +45,7 @@ sed -i.bak 's/-t ${THREADS} / /' ${SCRIPT_DIR}/TEstrainer/TEstrainer
 # Add SCRIPT_DIR to correct path
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${PACKAGE_HOME}/earlGrey
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${PACKAGE_HOME}/earlGreyLibConstruct
+sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${PACKAGE_HOME}/earlGreyAnnotationOnly
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/rcMergeRepeat*
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/headSwap.sh
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/autoPie.sh
@@ -53,6 +55,7 @@ sed -i.bak "s|STRAIN_SCRIPTS=.*|STRAIN_SCRIPTS=${SCRIPT_DIR}/TEstrainer/scripts/
 # Set permissions to files
 chmod +x ${PACKAGE_HOME}/earlGrey
 chmod +x ${PACKAGE_HOME}/earlGreyLibConstruct
+chmod +x ${PACKAGE_HOME}/earlGreyAnnotationOnly
 chmod +x ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
 chmod +x ${SCRIPT_DIR}/* > /dev/null 2>&1
 chmod +x ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7/ltr_finder
@@ -79,3 +82,4 @@ echo "unset PERL5LIB" >> "${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}_deactivat
 cd ${PREFIX}/bin
 ln -sf ${PACKAGE_HOME}/earlGrey .
 ln -sf ${PACKAGE_HOME}/earlGreyLibConstruct .
+ln -sf ${PACKAGE_HOME}/earlGreyAnnotationOnly .