Fix version checking with local installation. Support python installa…

…tion with conda in addition to pip. Build fixes for new CloudBioLinux release

cloudbio/custom/versioncheck.py

@@ -10,10 +10,10 @@
 
 from cloudbio.custom import shared
 
-def _parse_from_stdoutflag(stdout, flag):
+def _parse_from_stdoutflag(out, flag):
     """Extract version information from a flag in verbose stdout.
     """
-    for line in stdout.split("\n"):
+    for line in out.split("\n") + out.stderr.split("\n"):
         if line.find(flag) >= 0:
             parts = [x for x in line.split() if not x.startswith(flag)]
             return parts[0]

config/perl-libs.yaml

@@ -203,7 +203,7 @@ cpan:
   - 'Bio::ASN1::EntrezGene'
   - 'Bio::Graphics'
   - 'Bio::Phylo'
-  - 'BioPerl'
+  - 'http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz'
   - 'Bio::Das'
   - 'Bio::GFF3::LowLevel'
 # Currently have problems building on CentOS

config/python-libs.yaml

@@ -25,11 +25,9 @@ pypi:
   - yolk
   # build
   - Pyrex
-  - virtualenv
   # concurrency/web
   - Twisted
   # science
-  - bcbio-nextgen
   - cutadapt
   - ruffus
   - DendroPy
@@ -49,7 +47,6 @@ pypi:
   # visualization
   - gnuplot-py
   - PIL
-  - pydot
   - pygooglechart
   - pypdf
   - reportlab
@@ -83,3 +80,4 @@ conda:
   #- pygraphviz
   #- pysparse
   #- sympy
+  #- pydot # references python 3-only pyparsing

fabfile.py

@@ -321,13 +321,20 @@ def _read_main_config():
 
 def _python_library_installer(config):
     """Install python specific libraries using easy_install.
+    Handles using isolated anaconda environments.
     """
-    version_ext = "-%s" % env.python_version_ext if env.python_version_ext else ""
-    env.safe_sudo("easy_install%s -U pip" % version_ext)
+    with quiet():
+        is_anaconda = env.safe_run("conda -V").startswith("conda")
+    if is_anaconda:
+        for pname in env.flavor.rewrite_config_items("python", config.get("conda", [])):
+            env.safe_run("conda install --yes {0}".format(pname))
+        cmd = env.safe_run
+    else:
+        version_ext = "-%s" % env.python_version_ext if env.python_version_ext else ""
+        env.safe_sudo("easy_install%s -U pip" % version_ext)
+        cmd = env.safe_sudo
     for pname in env.flavor.rewrite_config_items("python", config['pypi']):
-        env.safe_sudo("{0} install --upgrade {1}".format(_pip_cmd(env), pname))
-    for pname in env.flavor.rewrite_config_items("python", config.get("conda", [])):
-        env.save_sudo("conda install {1}".format(pname))
+        cmd("{0} install --upgrade {1}".format(_pip_cmd(env), pname))
 
 def _ruby_library_installer(config):
     """Install ruby specific gems.