install script updates and docs v0.1.7

Author: Jon Palmer

docs/mac_install.md

@@ -47,14 +47,14 @@ brew install funannotate
 ```
 #download RepeatMasker libraries and install
 wget --user name --password pass http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/repeatmaskerlibraries-20150807.tar.gz
-tar zxvf repeatmaskerlibraries-20150807.tar.gz -C /usr/local/Cellar/repeatmasker/4.0.5/libexec
+tar zxvf repeatmaskerlibraries-20150807.tar.gz -C /usr/local/opt/repeatmasker/libexec
 
 #now setup RepeatMasker
-cd /usr/local/Cellar/repeatmasker/4.0.5/libexec
+cd /usr/local/opt/repeatmasker/libexec
 ./configure <config.txt
 
 #softlink GFF script to bin in path
-ln /usr/local/Cellar/repeatmasker/4.0.5/libexec/util/rmOutToGFF3.pl /usr/local/bin
+ln /usr/local/opt/repeatmasker/libexec/util/rmOutToGFF3.pl /usr/local/bin
 ```
 
 7) Download and install GeneMark-ES/ET [here](http://exon.gatech.edu/GeneMark/license_download.cgi)
@@ -73,16 +73,16 @@ cp $HOME/Downloads/gm_key ~/.gm_key
 export PATH="/usr/local/gmes_petap:$PATH"
 
 #add environmental variables
-export AUGUSTUS_CONFIG_PATH=/usr/local/Cellar/opt/augustus/libexec/config
-export EVM_HOME=/usr/local/Cellar/evidencemodeler/1.1.2
+export AUGUSTUS_CONFIG_PATH=/usr/local/opt/augustus/libexec/config
+export EVM_HOME=/usr/local/opt/evidencemodeler
 export GENEMARK_PATH=/usr/local/gmes_petap
-export BAMTOOLS_PATH=/usr/local/Cellar/bamtools/2.4.0/bin
+export BAMTOOLS_PATH=/usr/local/opt/bamtools/bin
 ```
 
 9) Re-launch a terminal window (or type `source ~/.bash_profile`). Finally run funannotate setup script to download databases and identify any problems.
 ```
 #navigate into funannotate install directory
-cd /usr/local/Cellar/funannotate/version#/libexec
+cd /usr/local/opt/funannotate/libexec
 
 #run setup script, might need sudo here
 ./setup.sh

docs/ubuntu_install.md

@@ -58,14 +58,14 @@ brew install funannotate
 6) Download RepeatMasker libraries from [RepBase](http://www.girinst.org/repbase/) you will need to register
 ```
 wget --user name --password pass http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/repeatmaskerlibraries-20150807.tar.gz
-tar zxvf repeatmaskerlibraries-20150807.tar.gz -C $HOME/.linuxbrew/Cellar/repeatmasker/4.0.5/libexec
+tar zxvf repeatmaskerlibraries-20150807.tar.gz -C $HOME/.linuxbrew/opt/repeatmasker/libexec
 
 #now setup RepeatMasker
-cd $HOME/.linuxbrew/repeatmasker/4.0.5/libexec
+cd $HOME/.linuxbrew/opt/repeatmasker/libexec
 ./configure <config.txt
 
 #softlink GFF script to bin
-ln -s $HOME/.linuxbrew/Cellar/repeatmasker/4.0.5/libexec/util/rmOutToGFF3.pl $HOME/.linuxbrew/bin
+ln -s $HOME/.linuxbrew/opt/repeatmaskerlibexec/util/rmOutToGFF3.pl $HOME/.linuxbrew/bin
 ```
 
 7) Download and install GeneMark-ES/ET [here](http://exon.gatech.edu/GeneMark/license_download.cgi)
@@ -89,18 +89,18 @@ export PATH="/usr/local/gmes_petap:$PATH"
 
 #add environmental variables
 export AUGUSTUS_CONFIG_PATH=$HOME/.linuxbrew/opt/augustus/libexec/config
-export EVM_HOME=$HOME/.linuxbrew/Cellar/evidencemodeler/1.1.2
+export EVM_HOME=$HOME/.linuxbrew/opt/evidencemodeler
 export GENEMARK_PATH=/usr/local/gmes_petap
-export BAMTOOLS_PATH=$HOME/.linuxbrew/Cellar/bamtools/2.4.0/bin
+export BAMTOOLS_PATH=$HOME/.linuxbrew/opt/bamtools/bin
 ```
 
 9) Re-launch a terminal window (or type `source ~/.bash_aliases`). Finally run funannotate setup script to download databases and identify any problems.
 ```
 #navigate into funannotate install directory
-cd $HOME/.linuxbrew/Cellar/funannotate/version#/libexec
+cd $HOME/.linuxbrew/opt/funannotate/libexec
 
-#run setup script, note you need sudo here to copy over the proper ProteinOrtho version
-sudo ./setup.sh
+#run setup script
+./setup.sh
 ```
 The script will download and format necessary databases and then check all of the dependencies of funannotate - any tool not properly installed will be flagged by the script.
 

setup.sh

@@ -32,16 +32,29 @@ else
     if [[ $dir == *"libexec"* ]]; then
         echo "HomeBrew installation detected, looking for any previous versions"
         pre_vers=$(ls ../../ | sort | tail -2 | head -1)
-        if [[ "$OSTYPE" == "darwin"* ]]; then
-            outputdir=$(readlink ../../$pre_vers/libexec/DB)
+        curr_vers=$(ls ../../ | sort | tail -1 | head -1)
+        if [ "$pre_vers" == "$curr_vers" ]; then
+            echo "This is the first HomeBrew install detected."
+            outputdir='/usr/local/share/funannotate'
+            echo -n "Default DB directory set to ($outputdir), continue [y/n]: "
+            read question1
+            if [ $question1 == 'n' ]; then
+                echo -n "Enter path to DB directory: "
+                read dbname
+                outputdir=$dbname
+            fi
         else
-            outputdir=$(readlink -f ../../$pre_vers/libexec/DB)
-        fi
-        echo "Symlink found to $outputdir, setting up DB"       
+            if [[ "$OSTYPE" == "darwin"* ]]; then
+                outputdir=$(readlink ../../$pre_vers/libexec/DB)
+            else
+                outputdir=$(readlink -f ../../$pre_vers/libexec/DB)
+            fi
+            echo "Symlink found to $outputdir, setting up DB"
+        fi    
     else
         echo "HomeBrew installation not detected, specify DB installation directory"
         outputdir='/usr/local/share/funannotate'
-        echo -n "DB directory set to ($outputdir), continue [y/n]: "
+        echo -n "Default DB directory set to ($outputdir), continue [y/n]: "
         read question1
         if [ $question1 == 'n' ]; then
             echo -n "Enter path to DB directory: "