Installation of HMMER Development Version: A Workaround For Little Endian Systems

easy_setup/install_ext_software/hmmer-devel.sh

@@ -0,0 +1,88 @@
+#!/usr/bin/env bash 
+
+# INSTALLING HMMER development version ##### 
+# HMMER: Sequence profile model generation using profile hidden Markov models 
+
+# HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. 
+# It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). 
+
+# http://hmmer.org/documentation.html 
+# HMMER and its documentation are freely distributed under the #3-Clause BSD open source license. 
+# For a copy of the license, see opensource.org/licenses/BSD-3-Clause. 
+
+
+###################### 
+### Housekeeping 
+
+shopt -s nocasematch # making comparisons case-insensitive 
+
+PARENT_PATH=$( cd "$(dirname "${BASH_SOURCE[0]}")" ; cd .. ; pwd -P ) # other files are located one directory above 
+. "$PARENT_PATH/configTRAL_path.cfg" || { # provide paths from config file 
+echo "configTRAL_path.cfg not found" 
+exit $? 
+} 
+
+###################### 
+### Download HMMER 
+
+## TODO: get full name of unzipped hmmer (with version) 
+
+for directory in "$TRAL_EXT_SOFTWARE/hmmer"*; do # test if hmmer files not already in directory 
+if [ -d "$directory" ]; then 
+echo "HMMER is already downloaded and in "$directory"" 
+else 
+{ 
+# LINK_HMMER="http://eddylab.org/software/hmmer/hmmer.tar.gz" # HHrepID Nov 22 2007 
+# wget "$LINK_HMMER" -P "$TRAL_EXT_SOFTWARE" # download execution file 
+# tar -xvzf "$TRAL_EXT_SOFTWARE/hmmer.tar.gz" -C "$TRAL_EXT_SOFTWARE" 
+# rm -rf "$TRAL_EXT_SOFTWARE/hmmer.tar.gz" 
+git clone https://github.com/EddyRivasLab/hmmer $TRAL_EXT_SOFTWARE 
+} || { 
+echo "Couldn't download HMMER." 
+exit $? 
+} 
+fi 
+done 
+
+###################### 
+### Compile and Install HMMER 
+
+{ 
+( 
+{ 
+cd $INSTALLATION_PATH/hmmer 
+mkdir -p lib/easel 
+git clone https://github.com/EddyRivasLab/easel lib/easel 
+(cd lib/easel; git checkout develop) 
+ln -s lib/easel/aclocal.m4 aclocal.m4 
+} && { 
+autoconf 
+./configure --prefix "$INSTALLATION_PATH" 
+# --build=ppc64le 
+make clean 
+make 
+# "$INSTALLATION_PATH"/bin make check # run a test suite 
+make install 
+} && { 
+echo "Installation of HMMER done." 
+ln -s "$INSTALLATION_PATH/bin/hmmbuild" "$INSTALLATION_PATH/hmmbuild" 
+echo -e "\nhmmbuild is in your path $INSTALLATION_PATH\n" 
+} 
+) 
+} || { 
+echo "Couldn't compile and install HMMER." 
+exit $? 
+} 
+
+###############i####### 
+### Uninstall HMMER 
+
+## TODO: find other way to delete hmmer and adapt it within uninstall script!! 
+
+# { 
+# ( cd "$TRAL_EXT_SOFTWARE/hmmer-"* && make uninstall ) 
+# rm -rf "$TRAL_EXT_SOFTWARE/hmmer-"* 
+# rm -rf "$INSTALLATION_PATH/hmmbuild" 
+# } || { 
+# echo -e "HMMER removed." 
+# } 

easy_setup/install_ext_software/hmmer.sh

@@ -65,7 +65,7 @@ done
         }
     )
     } || {
-    echo "Couldn't compile and install HMMER."
+    echo "Couldn't compile and install HMMER. Try to manually install the development version of HMMER by running hmmer-devel.sh which provides little endian support."
     exit $?
 }
 
@@ -80,4 +80,4 @@ done
 #     rm -rf "$INSTALLATION_PATH/hmmbuild"
 # } || {
 #     echo -e "HMMER removed."
-# }
+# }