Implement framework for adding wine based applications packaged using…

… this work - https://github.com/jmchilton/proteomics-wine-env.

Use this framework to implement installation code for the Proteowizard suite and multiplierz.

cloudbio/custom/bio_proteomics_wine.py

@@ -0,0 +1,66 @@
+from fabric.api import put, cd, run
+from fabric.contrib.files import exists
+
+from shared import (_make_tmp_dir, _fetch_and_unpack, _get_install, _make_copy, _write_to_file, _get_bin_dir)
+
+import os
+
+
+def install_proteomics_wine_env(env):
+    script_src = env.get("setup_proteomics_wine_env_script")
+    script_dest = "%s/bin" % env.get("system_install")
+    if not exists(script_dest):
+        put(script_src, script_dest, mode=0755, use_sudo=True)
+
+
+def install_multiplierz(env):
+    """
+    Assumes your wine environment contains an install Python 2.6
+    in C:\Python26.
+    """
+    wine_user = _get_wine_user(env)
+    env.safe_sudo("setup_proteomics_wine_env.sh", user=wine_user)
+    with _make_tmp_dir() as work_dir:
+        with cd(work_dir):
+            _fetch_and_unpack("hg clone http://multiplierz.hg.sourceforge.net:8000/hgroot/multiplierz/multiplierz")
+            with cd("multiplierz"):
+                wine_prefix = _get_wine_prefix(env)
+                env.safe_sudo("%s; wine %s/drive_c/Python26/python.exe setup.py install" % (_conf_wine(env), wine_prefix), user=wine_user)
+
+
+def install_proteowizard(env):
+    url = "http://teamcity.labkey.org:8080/repository/download/bt36/65129:id/pwiz-bin-windows-x86-vc100-release-3_0_3947.tar.bz2?guest=1"
+    install_dir = env.get("install_dir")
+    share_dir = "%s/share/proteowizard" % install_dir
+    with _make_tmp_dir() as work_dir:
+        with cd(work_dir):
+            _fetch_and_unpack(url, need_dir=False)
+            env.safe_sudo("cp -r . '%s'" % share_dir)
+    proteowizard_apps = ["msconvert", "msaccess", "chainsaw", "msdiff", "mspicture", "mscat", "txt2mzml", "MSConvertGUI", "Skyline", "Topograph", "SeeMS"]
+    for app in proteowizard_apps:
+        setup_wine_wrapper(env, "%s/%s" % (share_dir, app))
+
+
+def setup_wine_wrapper(env, to):
+    basename = os.path.basename(to)
+    contents = """#!/bin/bash
+setup_proteomics_wine_env.sh
+export WINEPREFIX=$HOME/.wine-proteomics
+wine %s "$@"
+""" % to
+    bin_dir = _get_bin_dir(env)
+    dest = "%s/%s" % (bin_dir, basename)
+    _write_to_file(contents, dest, 0755)
+
+
+def _conf_wine(env):
+    return "export WINEPREFIX=%s" % _get_wine_prefix(env)
+
+
+def _get_wine_prefix(env):
+    wine_user = _get_wine_user(env)
+    return "~%s/.wine-proteomics" % wine_user
+
+
+def _get_wine_user(env):
+    return env.get("wine_user", env.get("user"))

config/custom.yaml

@@ -71,6 +71,10 @@ bio_proteomics:
   - idpqonvert
   - pepitome
   - percolator
+bio_proteomics_wine:
+  - proteomics_wine_env
+  - multiplierz
+  - proteowizard
 cloudman:
   - nginx
   - proftpd

config/packages.yaml

@@ -399,18 +399,20 @@ bio_microarray:
 bio_visualization:
   - rasmol
   # - bio-linux-clcsequenceviewer # Awaiting fix
+bio_proteomics:
+  # Needed for TPP
+  - xsltproc
+  - libxml-sax-expat-perl
+  - libgd2-xpm-dev
+bio_proteomics_wine:
+  - wine
 bio_utils:
   - bio-linux-genquery
   - bio-linux-keyring
   - bio-linux-bldp-files
   - bio-linux-sampledata
   - bio-linux-taxinspector
   - bio-linux-xcut
-bio_proteomics:
-  # Needed for TPP
-  - xsltproc
-  - libxml-sax-expat-perl
-  - libgd2-xpm-dev
 phylogeny_testing:
   # new packages in testing (Debian 'wheezy')
   all: