Merge pull request #15 from martinghunt/change_to_pyfastaq

Change to pyfastaq; add to pypi

README.md

@@ -8,17 +8,10 @@ Installation
 
 Prerequisites:
   * [NCBI BLAST] [NCBI BLAST] blast+, and optionally blastall, installed and their commands in your path
-  * [Fastaq] [Fastaq] >= v0.1
-  * [Farmpy] [Farmpy] >= v0.2
 
-Once the prerequisites are installed, run the tests:
+Once the prerequisites are installed, install with pip:
 
-    python3 setup.py test
-
-Note that the tests check that blast+ is installed, but not blastall because it is optional.
-If all was OK, then install:
-
-    python3 setup.py install
+    pip3 install farm_blast
 
 Synopsis
 --------
@@ -48,5 +41,3 @@ To get all the options, use --help:
     farm_blast --help
 
 [NCBI BLAST]: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
-[Fastaq]: https://github.com/sanger-pathogens/Fastaq
-[Farmpy]: https://github.com/sanger-pathogens/Farmpy

farm_blast/utils.py

@@ -1,4 +1,4 @@
-from fastaq import utils
+from pyfastaq import utils
 import sys
 
 class Error (Exception): pass

setup.py

@@ -1,21 +1,44 @@
 import os
+import shutil
+import sys
 import glob
 from setuptools import setup, find_packages
 
-def read(fname):
-    return open(os.path.join(os.path.dirname(__file__), fname)).read()
+
+required_progs = [
+    'blastn',
+    'tblastn',
+    'tblastx',
+    'blastp',
+    'blastx',
+    'deltablast'
+]
+
+found_all_progs = True
+print('Checking blast+ programs found in path:')
+for program in required_progs:
+    if shutil.which(program) is None:
+        found_all_progs = False
+        found = ' NOT FOUND'
+    else:
+        found = ' OK'
+    print(found, program, sep='\t')
+
+if not found_all_progs:
+    print('Cannot install because some programs from the blast+ package not found.', file=sys.stderr)
+    sys.exit(1)
+
 
 setup(
-    name='Farm_blast',
-    version='0.1.1',
+    name='farm_blast',
+    version='0.1.2',
     description='Package to run blast in parallel on a compute farm',
-    long_description=read('README.md'),
     packages = find_packages(),
     author='Martin Hunt',
     author_email='[email protected]',
     url='https://github.com/sanger-pathogens/Farm_blast',
     scripts=glob.glob('scripts/*'),
     test_suite='nose.collector',
-    install_requires=['nose >= 1.3', 'fastaq >= 1.2', 'farmpy >= 0.2'],
+    install_requires=['nose >= 1.3', 'pyfastaq >= 3.0.1', 'farmpy >= 0.2'],
     license='GPLv3',
 )