Merge pull request #19 from gtamazian/binary-package

Routines and fixes for bionary packages

README.md

@@ -21,6 +21,24 @@ Cookiecutter is designed for use on Linux/UNIX and OS X systems.
 
 ## Installation
 
+You may install Cookiecutter from a binary package or compile it from
+source codes.
+
+### Binary package
+
+Unpack the downloaded archive using tar:
+
+```
+tar -xvzf cookiecutter_osx.tar.gz
+```
+
+Executable files are located in the `bin` subdirectory. You may 
+either launch Cookiecutter from the directory to which the archive was 
+unpacked or copy executable files to any directory specified in the 
+`PATH` variable of your environment.
+
+### Source codes
+
 The package should be compiled from its source code using the 
 provided Makefile in the following way.
 

create_package.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+
+set -eu
+set -o pipefail
+
+if [ $# -lt 1 ]; then
+	echo Please specify the output file name.
+	echo For example: ./create_package ~/Desktop/cookiecutter_osx.tar.gz 
+	exit 1
+fi
+
+OUTPUT_FILE="$1"
+PACKAGE_NAME=$( basename "$OUTPUT_FILE" )
+PACKAGE_NAME=$( echo "$PACKAGE_NAME" | sed "s/\..*//" )
+
+TEMPDIR=$( mktemp -d "/tmp/${PACKAGE_NAME}.XXXXXX" ) || exit 1
+
+# compile binary files
+cd src
+make
+cd ..
+
+# copy executable files
+mkdir "${TEMPDIR}/bin"
+for FILE in cookiecutter extract remove separate rm_reads; do
+	cp "./src/${FILE}" "${TEMPDIR}/bin/${FILE}"
+done
+
+# copy demo and data directories
+for DIR in data demo; do
+	cp -R "$DIR" "${TEMPDIR}/${DIR}"
+done
+
+# adjust the path for executable files in the demo script
+sed -i "s#default='.'#default='..\/bin/'#" \
+	${TEMPDIR}/demo/run_demo_analysis.py
+
+# copy LICENSE and README files
+for FILE in LICENSE README.md; do
+	cp "$FILE" "${TEMPDIR}/${FILE}"
+done
+
+# create a gzipped TAR archive
+TEMPFILE=$( tempfile )
+tar -C "/tmp" -cvf "${TEMPFILE}.tar" $( basename "$TEMPDIR" )
+gzip -9 "${TEMPFILE}.tar"
+mv "${TEMPFILE}.tar.gz" "$OUTPUT_FILE"
+
+# remove compiled files
+cd src
+make clean
+cd ..
+
+rm -r "$TEMPDIR"
+

demo/run_demo_analysis.py

@@ -30,12 +30,17 @@
     parser.add_argument('-c', '--clear', action='store_true',
                         help='remove files created by the demo')
 
+    parser.add_argument('-e', '--executable', default='.',
+                        help='the path to the Cookiecutter executable '
+                             'file')
+
     args = parser.parse_args()
 
     fastq_file1 = args.fastq1
     fastq_file2 = args.fastq2
 
     data = {
+        "cookiecutter": os.path.join(args.executable, 'cookiecutter'),
         "fastq1": fastq_file1,
         "fastq2": fastq_file2,
         "output_dir_1a": "../demo/temp_results_remove",
@@ -54,16 +59,16 @@
                          e='removing alpha satDNA')
 
     command_launches = dict(
-        a='cookiecutter remove -1 %(fastq1)s -2 %(fastq2)s -o %('
+        a='%(cookiecutter)s remove -1 %(fastq1)s -2 %(fastq2)s -o %('
           'output_dir_1a)s --fragments ../data/illumina.dat',
-        b='cookiecutter rm_reads -1 %(fastq1)s -2 %(fastq2)s -o %('
+        b='%(cookiecutter)s rm_reads -1 %(fastq1)s -2 %(fastq2)s -o %('
           'output_dir_1b)s --polygc 13 --length 50 --fragments '
           '../data/illumina.dat --dust_cutoff 3 --dust_k 4 --dust',
-        c='cookiecutter remove -i %(fastq1)s -o %('
+        c='%(cookiecutter)s remove -i %(fastq1)s -o %('
           'output_dir_1c)s --fragments ../data/rdna.dat',
-        d='cookiecutter extract -1 %(fastq1)s -2 %(fastq2)s -o %('
+        d='%(cookiecutter)s extract -1 %(fastq1)s -2 %(fastq2)s -o %('
           'output_dir_1d)s --fragments ../data/mtdna.dat',
-        e='cookiecutter separate -1 %(fastq1)s -2 %(fastq2)s -o %('
+        e='%(cookiecutter)s separate -1 %(fastq1)s -2 %(fastq2)s -o %('
           'output_dir_1e)s --fragments ../data/alpha.dat'
     )
 

src/cookiecutter

@@ -433,19 +433,14 @@ def verify_binaries():
     Check if Cookiecutter binaries are present in the same directory
     that contains the wrapper script.
     """
-    for i in program_names.itervalues():
-        path = os.path.join(os.path.dirname(os.path.realpath(
-            __file__)), i)
-        if not os.path.isfile(path) or not os.access(path, os.X_OK):
-            return False
-
     wrapper_path = os.path.dirname(os.path.realpath(__file__))
-    # if binaries are present in the PATH directory, mofity the way
-    # they are called
+
     for i in program_names.keys():
-        if not is_path_binary(program_names[i]):
-            program_names[i] = os.path.join(wrapper_path,
-                                            program_names[i])
+        path = os.path.join(wrapper_path, program_names[i])
+        if not os.path.isfile(path) or not os.access(path, os.X_OK):
+            return False
+        else:
+            program_names[i] = path
 
     return True
 
@@ -717,8 +712,11 @@ def cookiecutter():
 
 if __name__ == '__main__':
     if not verify_binaries():
-        message = 'Missing Cookiecutter binaries, please ' \
-                  'install the program using \'make && make ' \
+        message = 'Error: missing Cookiecutter binaries! If you use a ' \
+                  'binary package, please check that all executable ' \
+                  'files are in the same directory with ' \
+                  'cookiecutter. If you downloaded source codes, ' \
+                  'please install the program using \'make && make ' \
                   'install\' or launch it in the source ' \
                   'directory after running \'make\'. If you do not have ' \
                   'privileges to install to the system directory, you may ' \