minor bug fixes and updates to docs

Author: Jon Palmer

README.md

@@ -32,7 +32,7 @@ To see the help menu, simply type `funannotate` in the terminal window.  Similar
 $  funannotate
 
 Usage:       funannotate <command> <arguments>
-version:     0.1.0
+version:     0.1.3
 
 Description: Funannotate is a genome prediction, annotation, and comparison pipeline.
     
@@ -52,8 +52,8 @@ Command:     clean          Find/remove small repetitive contigs
 move into the `sample_data` directory of funannotate.
 
 ```
-#for example, funannotate installed in /usr/local/funannotate
-$ cd /usr/local/funannotate/sample_data
+#for example, funannotate installed in $HOMEBREW/Cellar/funannotate/0.1.3/libexec
+$ cd $HOMEBREW/Cellar/funannotate/0.1.3/libexecsample_data
 
 #run funannotate predict on genome 1
 $ funannotate predict -i genome1.fasta -o genome1 -s "Genome one" \

docs/mac_install.md

@@ -67,17 +67,17 @@ 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/1.1.1
+export EVM_HOME=/usr/local/Cellar/evidencemodeler/1.1.2
 export GENEMARK_PATH=/usr/local/gmes_petap
 export BAMTOOLS_PATH=/usr/local/Cellar/bamtools/2.4.0/bin
 ```
 
 8) 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/0.1.1/libexec
+cd /usr/local/Cellar/funannotate/0.1.3/libexec
 
-#run setup script
+#run setup script, might need sudo here
 ./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.

docs/ubuntu_install.md

@@ -83,11 +83,11 @@ cp $HOME/Downloads/gm_key_64 ~/.gm_key
 #example using gedit
 sudo gedit ~/.bash_aliases
 
-#add folders to PATH
-export PATH="/usr/local/funannotate:/usr/local/GAG:/usr/local/gmes_petap:/usr/local/BRAKER1:/usr/local/tRNAscan-SE-1.3.1:/opt/augustus-3.2.1/bin:$PATH"
+#add folder for GeneMark to PATH, HomeBrew will take care of other tools
+export PATH="/usr/local/gmes_petap:$PATH"
 
 #add environmental variables
-export AUGUSTUS_CONFIG_PATH=/opt/augustus-3.2.1/config
+export AUGUSTUS_CONFIG_PATH=$HOME/.linuxbrew/opt/augustus/libexec/config
 export EVM_HOME=$HOME/.linuxbrew/Cellar/evidencemodeler/1.1.2
 export GENEMARK_PATH=/usr/local/gmes_petap
 export BAMTOOLS_PATH=$HOME/.linuxbrew/Cellar/bamtools/2.4.0/bin
@@ -96,9 +96,9 @@ export BAMTOOLS_PATH=$HOME/.linuxbrew/Cellar/bamtools/2.4.0/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 /usr/local/funannotate
+cd $HOME/.linuxbrew/Cellar/funannotate/0.1.3/libexec
 
-#run setup script, not you need sudo here to copy over the proper ProteinOrtho version
+#run setup script, note you need sudo here to copy over the proper ProteinOrtho version
 sudo ./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.

funannotate.py

@@ -31,7 +31,7 @@ def fmtcols(mylist, cols):
              for i in range(0,num_lines))
     return "\n".join(lines)
 
-version = '0.1.2'
+version = '0.1.3'
 
 default_help = """
 Usage:       funannotate <command> <arguments>

lib/library.py

@@ -834,7 +834,6 @@ def ParseErrorReport(input, Errsummary, val, Discrep, output):
                         remove.append(tRNA)
                         remove.append(exon)
         remove = set(remove)
-        print remove
         remove_match = re.compile(r'\b(?:%s)+\b' % '|'.join(remove))
         with open(output, 'w') as out:
             with open(input, 'rU') as GFF:

setup.sh

@@ -44,8 +44,8 @@ if [ "$db" = 'pass' ]; then
     #check if Merops is already downloaded
     if [ ! -f merops_formatted.fa ]; then
         echo "You need to manually download the MEROPS protease database as it requires a log in"
-        echo "download: merops_scan.lib.txt   from here: https://merops.sanger.ac.uk/download/"
-        echo "then move the file into the funnanotate DB folder, once the file is in the folder the script will proceed."
+        echo "download: merops_scan.lib   from here: https://merops.sanger.ac.uk/download/"
+        echo "then move the file into /usr/local/share/funannotate, once the file is in the folder the script will proceed."
         until [ -f merops_scan.lib ]
         do
              sleep 5