Merge pull request #24 from sanger-pathogens/RT664678_more_container_…

…fixes

RT664678 in production, assume farm_blast executable is in path

.travis.yml

@@ -1,12 +1,7 @@
 language: python
-branches:
-  only:
-  - master
 python:
   - "3.7"
 sudo: false
-install:
-  - source ./install_dependencies.sh
 before_script:
   - pip install codecov
 script:

farm_blast/pipeline.py

@@ -242,7 +242,7 @@ def _make_combine_script(self, script_name=None):
         if self.test:
             print(self.farm_blast_script, '--test --fix_coords_in_blast_output x x', file=f)
         else:
-            print(self.farm_blast_script, '--fix_coords_in_blast_output x x', file=f)
+            print('farm_blast --fix_coords_in_blast_output x x', file=f)
         print('rm', ' '.join(self.files_to_delete), file=f)
         print('touch FINISHED', file=f)
         f.close()

setup.py

@@ -25,8 +25,7 @@
     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)
+    print('Some programs from the blast+ package not found, farm_blast may not work properly.', file=sys.stderr)
 
 
 setup(