Merge branch 'master' of github.com:BIMSBbioinfo/pigx_bsseq

.gitignore

@@ -7,6 +7,7 @@
 *~
 
 # autoconf generated files
+qsub-template.sh
 configure
 config.status
 pigx-bsseq

Makefile.am

@@ -4,7 +4,8 @@ nodist_bin_SCRIPTS = \
   pigx-bsseq
 
 dist_pkglibexec_SCRIPTS =			\
-  BSseq_pipeline.py
+  BSseq_pipeline.py					\
+  qsub-template.sh
 
 pkglibexec_scriptsdir = $(pkglibexecdir)/scripts
 dist_pkglibexec_scripts_SCRIPTS =	\

VERSION

@@ -1 +1 @@
-0.0.8
+0.0.9

configure.ac

@@ -79,10 +79,22 @@ AX_COMPARE_VERSION([$SAMTOOLS_VERSION], [lt], [$SAMTOOLS_VERSION_MIN],
       [AC_MSG_ERROR([Please install Samtools $SAMTOOLS_VERSION_MIN.])])
   ])
 
+AC_ARG_ENABLE([environment-capture],
+  AS_HELP_STRING([--disable-environment-capture], [Do not capture environment variables.]),
+  [AC_MSG_NOTICE([Environment variables will not be captured.])],
+  [dnl
+AC_MSG_NOTICE([Environment variables will be captured.])
+capture_environment=yes
+AC_ARG_VAR(R_LIBS_SITE, The search path for all R packages)
+AC_ARG_VAR(PYTHONPATH, The search path for all Python packages)
+  ])
+
+AC_SUBST([capture_environment])
 AC_CONFIG_FILES([etc/settings.yaml
                  report_templates/index.Rmd
                  report_templates/diffmeth.Rmd
-                 Makefile])
+                 Makefile
+                 qsub-template.sh])
 AC_CONFIG_FILES([test.sh], [chmod +x test.sh])
 AC_CONFIG_FILES([pigx-bsseq], [chmod +x pigx-bsseq])
 

m4/ax_r_package.m4

@@ -48,7 +48,7 @@ AC_DEFUN([AX_R_PACKAGE], [
 
     if test -n "VERSION"
     then
-      TEST=$( $R --silent --vanilla -e 'if(!(packageDescription("PKG")$Version >= "VERSION")) stop("not found")' 2>/dev/null )
+      TEST=$( $R --silent --vanilla -e 'if(compareVersion(packageDescription("PKG")$Version, "VERSION") < 0) { stop("not found") }' 2>/dev/null )
       AS_IF([test $? -eq 0], [], [
         AC_MSG_RESULT([no])
         AC_MSG_ERROR([You need at least version VERSION of the R package PKG.])

pigx-bsseq.in

@@ -22,7 +22,17 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-
+if 'yes' == '@capture_environment@':
+    import os, sys
+    os.environ["R_LIBS_SITE"] = "@R_LIBS_SITE@"
+    os.environ["PYTHONPATH"] = "@PYTHONPATH@"
+    # Setting PYTHONPATH does not help with dependencies needed for
+    # this script.
+    for directory in "@PYTHONPATH@".split(":"):
+        try:
+            sys.path.index(directory)
+        except ValueError:
+            sys.path.insert(1, directory)
 
 
 import argparse
@@ -325,7 +335,7 @@ def prepare_links():
         contents = path.join(where, 'etc/CONTENTS.txt')
     else:
         contents = path.join(config['locations']['pkgdatadir'], 'CONTENTS.txt')
-    shutil.copy(contents, path.join(config['locations']['output-dir'], 'pigx_work/'))
+    shutil.copyfile(contents, path.join(config['locations']['output-dir'], 'pigx_work/CONTENTS.txt'))
 
     # Link the reference genome
     try:
@@ -491,12 +501,13 @@ if config['execution']['submit-to-cluster']:
             exit(1)
         else:
             raise
-    qsub = "qsub -V  %s -l h_stack={cluster.h_stack} -l h_vmem={cluster.MEM} %s -b y -pe smp {cluster.nthreads} -cwd" % ( queue_selection_string, contact_email_string)
+    qsub = "qsub -v R_LIBS_USER -v PATH -v GUIX_LOCPATH  %s -l h_stack={cluster.h_stack} -l h_vmem={cluster.MEM} %s -b y -pe smp {cluster.nthreads} -cwd" % ( queue_selection_string, contact_email_string)
     if config['execution']['cluster']['args']:
         qsub += " " + config['execution']['cluster']['args']
     command += [
         "--cluster-config={}".format(cluster_config_file),
         "--cluster={}".format(qsub),
+        "--jobscript={}/qsub-template.sh".format(config['locations']['pkglibexecdir']),
         "--latency-wait={}".format(config['execution']['cluster']['missing-file-timeout'])
     ]
 else:

qsub-template.sh.in

@@ -0,0 +1,11 @@
+#!@GNUBASH@
+# properties = {properties}
+
+if [ 'yes' = '@capture_environment@' ]; then
+    export R_LIBS_SITE="@R_LIBS_SITE@"
+    export PYTHONPATH="@PYTHONPATH@"
+fi
+
+env
+
+{exec_job}