Update Earl Grey build.sh (#51324)

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update build.sh

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}/earlGreyAnnotationOnly  #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}/earlGreyAnnotationOnly ${SCRIPT_DIR}/rcMergeRepeat* ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
 
 
 # Remove -pa from RepeatClassifier
@@ -44,15 +45,17 @@ 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" ${SCRIPT_DIR}/autoPie.sh
-sed -i.bak "s|INSERT_FILENAME_HERE|${SCRIPT_DIR}/TEstrainer/scripts/|g" ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
+sed -i.bak "s|STRAIN_SCRIPTS=.*|STRAIN_SCRIPTS=${SCRIPT_DIR}/TEstrainer/scripts/|g" ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
 
 
 # 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 .

recipes/earlgrey/meta.yaml

@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   skip: True # [osx]
   run_exports:
     - {{ pin_subpackage('earlgrey', max_pin='x') }}