Add NGSPlotDB-hg19-data recipe

recipes/r-ngsplot-hg19/meta.yaml

@@ -0,0 +1,20 @@
+{% set version = "3.00" %}
+{% set name = "ngsplotdb-hg19" %}
+
+package:
+  name: 'ngsplotdb-{{ name|lower }}'
+  version: '{{ version }}'
+build:
+  number: 0
+requirements:
+  run:
+    - r-ngsplot
+    - r-base
+    - wget
+test:
+  commands:
+    - (ngsplotdb.py list | grep -qF "hg19" || ngsplotdb.py list)
+about:
+  home: 'https://github.com/shenlab-sinai/ngsplot'
+  license: GPL-2.0
+  summary: 'HG19 genome database for NGSplot'

recipes/r-ngsplot-hg19/post-link.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+FN="ngsplotdb_hg19_75_3.00.tar.gz"
+URLS=(
+  "https://drive.google.com/uc?export=download&id=0B5hDZ2BucCI6SURYWW5XdUxnbW8"
+)
+MD5="172a6a93de3d1ae8a3ad6d6d79e911f7"
+
+# Use a staging area in the conda dir rather than temp dirs, both to avoid
+# permission issues as well as to have things downloaded in a predictable
+# manner.
+STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+mkdir -p $STAGING
+TARBALL=$STAGING/$FN
+
+SUCCESS=0
+for URL in ${URLS[@]}; do
+  wget -O- -q ${URL} > $TARBALL
+  [[ $? == 0 ]] || continue
+
+  # Platform-specific md5sum checks.
+  if [[ $(uname -s) == "Linux" ]]; then
+    if md5sum -c <<<"$MD5  $TARBALL"; then
+      SUCCESS=1
+      break
+    fi
+  else if [[ $(uname -s) == "Darwin" ]]; then
+    if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then
+      SUCCESS=1
+      break
+    fi
+  fi
+fi
+done
+
+if [[ $SUCCESS != 1 ]]; then
+  echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" >> "${PREFIX}/.messages.txt" 2>&1
+  printf '%s\n' "${URLS[@]}" >> "${PREFIX}/.messages.txt" 2>&1
+  exit 1
+fi
+
+# Install and clean up
+ngsplotdb.py install "${TARBALL}" >> "${PREFIX}/.messages.txt" 2>&1
+rm $TARBALL
+rmdir $STAGING

recipes/r-ngsplot-hg19/pre-unlink.sh

@@ -0,0 +1 @@
+ngsplotdb.py remove hg19 >> "${PREFIX}/.messages.txt" 2>&1

recipes/r-ngsplot/build.sh

@@ -2,10 +2,18 @@
 outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 mkdir -p $outdir
 mkdir -p $PREFIX/bin
-cp -R * $outdir 
-#Set up links for 
-for f in $outdir/*; do
-    ln -s $outdir/* $PREFIX/bin
-    fbname=$(basename "$f")
-    chmod 0755 ${PREFIX}/bin/$fbname
-done
+cp -R {bin,database,example,galaxy,lib,LICENSE} ${outdir}/
+# Set up links for 
+for f in ${outdir}/bin/*; do
+    ln -s ${f} ${PREFIX}/bin
+done
+
+# Patch scripts to use proper path and not depend on NGSPLOT env variable
+for f in "${outdir}"/bin/*.py ; do
+    sed -Ei.bak "s|os\.environ\[\"NGSPLOT\"\]|\"${outdir}\"|g" "${f}"
+    rm "${f}.bak"
+done
+for f in "${outdir}"/bin/{,backup}/*.r ; do
+    sed -Ei.bak "s|Sys\.getenv\('NGSPLOT'\)|\"${outdir}\"|g" "${f}"
+    rm "${f}.bak"
+done

recipes/r-ngsplot/meta.yaml

@@ -9,7 +9,6 @@ source:
 
 build:
   number: 0
-  skip: True 
   rpaths:
     - lib/R/lib/
     - lib/
@@ -23,13 +22,12 @@ requirements:
     - bioconductor-rsamtools
     - bioconductor-bsgenome
     - bioconductor-shortread
+    - python <3.0a0
 
 test:
   commands:
-    - ngsplotdb.py list | true
-    - ngs.plot.r 2>&1 | true
-    - replot.r 2>&1 | true
-    - plotCorrGram.r 2>&1 | true
+    - (ngsplotdb.py list 2>&1 | grep -qF "your ngs.plot database may be corrupted." || ngsplotdb.py list)
+    - (ngs.plot.r | grep -qF "Visit https://github.com/shenlab-sinai/ngsplot/wiki/ProgramArguments101 for details" || ngs.plot.r)
 
 about:
   license: GPL-2.0