From f0180d74669203383385986e92291306f8e75d4f Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Tue, 5 Jun 2018 21:05:34 +0200
Subject: [PATCH 01/31] Add NGSPlotDB-hg19-data recipe

---
 recipes/r-ngsplot-hg19/meta.yaml     | 29 ++++++++++++++++++
 recipes/r-ngsplot-hg19/post-link.sh  | 44 ++++++++++++++++++++++++++++
 recipes/r-ngsplot-hg19/pre-unlink.sh |  1 +
 3 files changed, 74 insertions(+)
 create mode 100644 recipes/r-ngsplot-hg19/meta.yaml
 create mode 100644 recipes/r-ngsplot-hg19/post-link.sh
 create mode 100644 recipes/r-ngsplot-hg19/pre-unlink.sh

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
new file mode 100644
index 0000000000000..078a464595630
--- /dev/null
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -0,0 +1,29 @@
+{% set version = "3.00" %}
+{% set name = "ngsplotdb-hg19" %}
+
+package:
+  name: 'ngsplotdb-{{ name|lower }}'
+  version: '{{ version }}'
+source:
+  fn: '{{ name }}_{{ version }}.tar.gz'
+  url:
+    - 'https://doc-0g-a0-docs.googleusercontent.com/docs/securesc/ha0ro937gcuc7l7deffksulhg5h7mbp1/jiksn2m41cm3dbspq0nqt102h6m6eo1o/1528221600000/01382619737792242945/*/0B5hDZ2BucCI6SURYWW5XdUxnbW8?e=download'
+  sha256: a3ad6daceec383f88faf3d3ee899f2bef37b3be2658ee9afa01e86404c0c92bd
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+requirements:
+  build:
+    - 'r-ngsplot'
+    - r-base
+  run:
+    - 'r-ngsplot'
+    - r-base
+    - wget
+
+about:
+  home: 'https://github.com/shenlab-sinai/ngsplot'
+  license: GPL-2.0
+  summary: 'Quick mining and visualization of NGS data by integrating genomic databases'
diff --git a/recipes/r-ngsplot-hg19/post-link.sh b/recipes/r-ngsplot-hg19/post-link.sh
new file mode 100644
index 0000000000000..68a317a42aac8
--- /dev/null
+++ b/recipes/r-ngsplot-hg19/post-link.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+FN="ngsplotdb_hg19_75_3.00.tar.gz"
+URLS=(
+  "https://doc-0g-a0-docs.googleusercontent.com/docs/securesc/ha0ro937gcuc7l7deffksulhg5h7mbp1/jiksn2m41cm3dbspq0nqt102h6m6eo1o/1528221600000/01382619737792242945/*/0B5hDZ2BucCI6SURYWW5XdUxnbW8?e=download"
+)
+sha256="a3ad6daceec383f88faf3d3ee899f2bef37b3be2658ee9afa01e86404c0c92bd"
+
+# 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 $MD5:"
+  printf '%s\n' "${URLS[@]}"
+  exit 1
+fi
+
+# Install and clean up
+ngsplotdb.py install ngsplotdb_hg19_75_3.00.tar.gz
+rm $TARBALL
+rmdir $STAGING
\ No newline at end of file
diff --git a/recipes/r-ngsplot-hg19/pre-unlink.sh b/recipes/r-ngsplot-hg19/pre-unlink.sh
new file mode 100644
index 0000000000000..d5a8311cd5e2c
--- /dev/null
+++ b/recipes/r-ngsplot-hg19/pre-unlink.sh
@@ -0,0 +1 @@
+ngsplotdb.py remove hg19
\ No newline at end of file

From f4d66f2d1ea03019a481dbfc4e85673a386cd651 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Tue, 5 Jun 2018 21:12:02 +0200
Subject: [PATCH 02/31] Okay, lets test this

---
 recipes/r-ngsplot-hg19/meta.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
index 078a464595630..3fe4a60d1927a 100644
--- a/recipes/r-ngsplot-hg19/meta.yaml
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -22,7 +22,9 @@ requirements:
     - 'r-ngsplot'
     - r-base
     - wget
-
+test:
+  commands:
+    - 'ngsplotdb.py install ngsplotdb-hg19_3.00.tar.gz | true'
 about:
   home: 'https://github.com/shenlab-sinai/ngsplot'
   license: GPL-2.0

From 1975340d5eeb6a590a33c8268f6448d954b7d92f Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 10:46:39 +0200
Subject: [PATCH 03/31] Add fix for ngsplot recipe

---
 recipes/r-ngsplot/meta.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/recipes/r-ngsplot/meta.yaml b/recipes/r-ngsplot/meta.yaml
index 9c570c1f1de8f..4ab9fac8987bb 100644
--- a/recipes/r-ngsplot/meta.yaml
+++ b/recipes/r-ngsplot/meta.yaml
@@ -9,7 +9,6 @@ source:
 
 build:
   number: 0
-  skip: True 
   rpaths:
     - lib/R/lib/
     - lib/

From e9bd34b4f0c66a4f20d9a7af96267ed354a881f0 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 12:27:57 +0200
Subject: [PATCH 04/31] Removed

---
 recipes/r-ngsplot-hg19/meta.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
index 3fe4a60d1927a..9d30ef21f0838 100644
--- a/recipes/r-ngsplot-hg19/meta.yaml
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -11,9 +11,6 @@ source:
   sha256: a3ad6daceec383f88faf3d3ee899f2bef37b3be2658ee9afa01e86404c0c92bd
 build:
   number: 0
-  rpaths:
-    - lib/R/lib/
-    - lib/
 requirements:
   build:
     - 'r-ngsplot'

From 3d214fbb222c68abc17c38e39686d6ef41581684 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 12:30:20 +0200
Subject: [PATCH 05/31] Added @mbargull 's suggestions

---
 recipes/r-ngsplot-hg19/meta.yaml    | 7 ++-----
 recipes/r-ngsplot-hg19/post-link.sh | 2 +-
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
index 9d30ef21f0838..53f259bfd8c4e 100644
--- a/recipes/r-ngsplot-hg19/meta.yaml
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -8,20 +8,17 @@ source:
   fn: '{{ name }}_{{ version }}.tar.gz'
   url:
     - 'https://doc-0g-a0-docs.googleusercontent.com/docs/securesc/ha0ro937gcuc7l7deffksulhg5h7mbp1/jiksn2m41cm3dbspq0nqt102h6m6eo1o/1528221600000/01382619737792242945/*/0B5hDZ2BucCI6SURYWW5XdUxnbW8?e=download'
-  sha256: a3ad6daceec383f88faf3d3ee899f2bef37b3be2658ee9afa01e86404c0c92bd
+  md5: 172a6a93de3d1ae8a3ad6d6d79e911f7
 build:
   number: 0
 requirements:
-  build:
-    - 'r-ngsplot'
-    - r-base
   run:
     - 'r-ngsplot'
     - r-base
     - wget
 test:
   commands:
-    - 'ngsplotdb.py install ngsplotdb-hg19_3.00.tar.gz | true'
+    - ngsplotdb.py install "${TARBALL}" > "${PREFIX}/.messages.txt" 2>&1
 about:
   home: 'https://github.com/shenlab-sinai/ngsplot'
   license: GPL-2.0
diff --git a/recipes/r-ngsplot-hg19/post-link.sh b/recipes/r-ngsplot-hg19/post-link.sh
index 68a317a42aac8..a3093047de37d 100644
--- a/recipes/r-ngsplot-hg19/post-link.sh
+++ b/recipes/r-ngsplot-hg19/post-link.sh
@@ -39,6 +39,6 @@ if [[ $SUCCESS != 1 ]]; then
 fi
 
 # Install and clean up
-ngsplotdb.py install ngsplotdb_hg19_75_3.00.tar.gz
+ngsplotdb.py install "${TARBALL}" > "${PREFIX}/.messages.txt" 2>&1
 rm $TARBALL
 rmdir $STAGING
\ No newline at end of file

From e486e499c5b60b0e84d0b461ee04d08190f6012a Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 12:30:59 +0200
Subject: [PATCH 06/31] More suggestions

---
 recipes/r-ngsplot-hg19/pre-unlink.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/r-ngsplot-hg19/pre-unlink.sh b/recipes/r-ngsplot-hg19/pre-unlink.sh
index d5a8311cd5e2c..5112073d6de92 100644
--- a/recipes/r-ngsplot-hg19/pre-unlink.sh
+++ b/recipes/r-ngsplot-hg19/pre-unlink.sh
@@ -1 +1 @@
-ngsplotdb.py remove hg19
\ No newline at end of file
+ngsplotdb.py remove hg19 > "${PREFIX}/.messages.txt" 2>&1
\ No newline at end of file

From f5af8a98905225b9a5da70dcd56941a0dc1cd1b2 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 12:31:37 +0200
Subject: [PATCH 07/31] Add suggestions of @mbargull

---
 recipes/r-ngsplot-hg19/post-link.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/post-link.sh b/recipes/r-ngsplot-hg19/post-link.sh
index a3093047de37d..d24691281ac40 100644
--- a/recipes/r-ngsplot-hg19/post-link.sh
+++ b/recipes/r-ngsplot-hg19/post-link.sh
@@ -33,8 +33,8 @@ fi
 done
 
 if [[ $SUCCESS != 1 ]]; then
-  echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:"
-  printf '%s\n' "${URLS[@]}"
+  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
 

From 3ead683ff9566784d9662194e34d1c4c287723f0 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 12:58:42 +0200
Subject: [PATCH 08/31] Adjusted build.sh script

---
 recipes/r-ngsplot/build.sh | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh
index 63d91bc0bcbe9..7210960b7481e 100644
--- a/recipes/r-ngsplot/build.sh
+++ b/recipes/r-ngsplot/build.sh
@@ -4,8 +4,7 @@ mkdir -p $outdir
 mkdir -p $PREFIX/bin
 cp -R * $outdir 
 #Set up links for 
-for f in $outdir/*; do
-    ln -s $outdir/* $PREFIX/bin
+for f in ${outdir}/bin/*; do
+    ln -s ${f} ${PREFIX}/bin
     fbname=$(basename "$f")
-    chmod 0755 ${PREFIX}/bin/$fbname
 done
\ No newline at end of file

From b1ae4754bb2f5095f90bd7b9be74a1af5dcaebfb Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 13:03:35 +0200
Subject: [PATCH 09/31] Removed source, as this is provided by post-link

---
 recipes/r-ngsplot-hg19/meta.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
index 53f259bfd8c4e..f9240e6c2d92b 100644
--- a/recipes/r-ngsplot-hg19/meta.yaml
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -5,9 +5,6 @@ package:
   name: 'ngsplotdb-{{ name|lower }}'
   version: '{{ version }}'
 source:
-  fn: '{{ name }}_{{ version }}.tar.gz'
-  url:
-    - 'https://doc-0g-a0-docs.googleusercontent.com/docs/securesc/ha0ro937gcuc7l7deffksulhg5h7mbp1/jiksn2m41cm3dbspq0nqt102h6m6eo1o/1528221600000/01382619737792242945/*/0B5hDZ2BucCI6SURYWW5XdUxnbW8?e=download'
   md5: 172a6a93de3d1ae8a3ad6d6d79e911f7
 build:
   number: 0

From cf5079427dd9edec73c8ee914cfc917b7bd89e13 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 13:16:07 +0200
Subject: [PATCH 10/31] Hopefully more permant file URL

---
 recipes/r-ngsplot-hg19/meta.yaml    | 2 +-
 recipes/r-ngsplot-hg19/post-link.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
index f9240e6c2d92b..335590ae044aa 100644
--- a/recipes/r-ngsplot-hg19/meta.yaml
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -19,4 +19,4 @@ test:
 about:
   home: 'https://github.com/shenlab-sinai/ngsplot'
   license: GPL-2.0
-  summary: 'Quick mining and visualization of NGS data by integrating genomic databases'
+  summary: 'HG19 genome database for NGSplot'
diff --git a/recipes/r-ngsplot-hg19/post-link.sh b/recipes/r-ngsplot-hg19/post-link.sh
index d24691281ac40..fed10174ce8b0 100644
--- a/recipes/r-ngsplot-hg19/post-link.sh
+++ b/recipes/r-ngsplot-hg19/post-link.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 FN="ngsplotdb_hg19_75_3.00.tar.gz"
 URLS=(
-  "https://doc-0g-a0-docs.googleusercontent.com/docs/securesc/ha0ro937gcuc7l7deffksulhg5h7mbp1/jiksn2m41cm3dbspq0nqt102h6m6eo1o/1528221600000/01382619737792242945/*/0B5hDZ2BucCI6SURYWW5XdUxnbW8?e=download"
+  "https://drive.google.com/uc?export=download&id=0B5hDZ2BucCI6SURYWW5XdUxnbW8"
 )
 sha256="a3ad6daceec383f88faf3d3ee899f2bef37b3be2658ee9afa01e86404c0c92bd"
 

From ae6e95af55ac60c1c02dc432521ef0d7d35e5d78 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 13:45:40 +0200
Subject: [PATCH 11/31] Double check

---
 recipes/r-ngsplot-hg19/meta.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
index 335590ae044aa..a5e3f82db1c1d 100644
--- a/recipes/r-ngsplot-hg19/meta.yaml
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -4,7 +4,6 @@
 package:
   name: 'ngsplotdb-{{ name|lower }}'
   version: '{{ version }}'
-source:
   md5: 172a6a93de3d1ae8a3ad6d6d79e911f7
 build:
   number: 0

From 159081417ceab9e5a574cce010d1450eae927718 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 14:40:27 +0200
Subject: [PATCH 12/31] Add check for hg19 database, removed sha256

---
 recipes/r-ngsplot-hg19/meta.yaml    | 3 +--
 recipes/r-ngsplot-hg19/post-link.sh | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
index a5e3f82db1c1d..f3ca75fc92579 100644
--- a/recipes/r-ngsplot-hg19/meta.yaml
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -4,7 +4,6 @@
 package:
   name: 'ngsplotdb-{{ name|lower }}'
   version: '{{ version }}'
-  md5: 172a6a93de3d1ae8a3ad6d6d79e911f7
 build:
   number: 0
 requirements:
@@ -14,7 +13,7 @@ requirements:
     - wget
 test:
   commands:
-    - ngsplotdb.py install "${TARBALL}" > "${PREFIX}/.messages.txt" 2>&1
+    - ngsplotdb.py list | grep "hg19" > "${PREFIX}/.messages.txt" 2>&1
 about:
   home: 'https://github.com/shenlab-sinai/ngsplot'
   license: GPL-2.0
diff --git a/recipes/r-ngsplot-hg19/post-link.sh b/recipes/r-ngsplot-hg19/post-link.sh
index fed10174ce8b0..63951db12efe9 100644
--- a/recipes/r-ngsplot-hg19/post-link.sh
+++ b/recipes/r-ngsplot-hg19/post-link.sh
@@ -3,7 +3,7 @@ FN="ngsplotdb_hg19_75_3.00.tar.gz"
 URLS=(
   "https://drive.google.com/uc?export=download&id=0B5hDZ2BucCI6SURYWW5XdUxnbW8"
 )
-sha256="a3ad6daceec383f88faf3d3ee899f2bef37b3be2658ee9afa01e86404c0c92bd"
+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

From e4eb39ec9c7a0e8992f0b174fe40bace966f7241 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 21:38:32 +0200
Subject: [PATCH 13/31] Better tests for ngsplot

---
 recipes/r-ngsplot/meta.yaml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/recipes/r-ngsplot/meta.yaml b/recipes/r-ngsplot/meta.yaml
index 4ab9fac8987bb..e06081f22c04e 100644
--- a/recipes/r-ngsplot/meta.yaml
+++ b/recipes/r-ngsplot/meta.yaml
@@ -25,10 +25,8 @@ requirements:
 
 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
+    - ngs.plot.r | grep -q "Visit https://github.com/shenlab-sinai/ngsplot/wiki/ProgramArguments101 for details"
 
 about:
   license: GPL-2.0

From 721e3a2cb6933a12d4b1c0621f9f0107df111b11 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 21:42:39 +0200
Subject: [PATCH 14/31] More specific copying

---
 recipes/r-ngsplot/build.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh
index 7210960b7481e..f84c136aa0248 100644
--- a/recipes/r-ngsplot/build.sh
+++ b/recipes/r-ngsplot/build.sh
@@ -2,9 +2,9 @@
 outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 mkdir -p $outdir
 mkdir -p $PREFIX/bin
-cp -R * $outdir 
+cp -R {bin,database,example,galaxy,lib,webings,LICENSE} ${outdir}/
 #Set up links for 
 for f in ${outdir}/bin/*; do
     ln -s ${f} ${PREFIX}/bin
     fbname=$(basename "$f")
-done
\ No newline at end of file
+done

From 054a918140cbedf0752773f9bae56e678f7d3983 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 21:43:00 +0200
Subject: [PATCH 15/31] Post and Pre Unlink scripts for r-ngsplot-hg19 updated

---
 recipes/r-ngsplot-hg19/post-link.sh  | 6 +++---
 recipes/r-ngsplot-hg19/pre-unlink.sh | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/post-link.sh b/recipes/r-ngsplot-hg19/post-link.sh
index 63951db12efe9..6e90b62cd4f35 100644
--- a/recipes/r-ngsplot-hg19/post-link.sh
+++ b/recipes/r-ngsplot-hg19/post-link.sh
@@ -14,7 +14,7 @@ TARBALL=$STAGING/$FN
 
 SUCCESS=0
 for URL in ${URLS[@]}; do
-  wget -O- -q $URL > $TARBALL
+  wget -O- -q ${URL} > $TARBALL
   [[ $? == 0 ]] || continue
 
   # Platform-specific md5sum checks.
@@ -33,7 +33,7 @@ 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
+  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
@@ -41,4 +41,4 @@ fi
 # Install and clean up
 ngsplotdb.py install "${TARBALL}" > "${PREFIX}/.messages.txt" 2>&1
 rm $TARBALL
-rmdir $STAGING
\ No newline at end of file
+rmdir $STAGING
diff --git a/recipes/r-ngsplot-hg19/pre-unlink.sh b/recipes/r-ngsplot-hg19/pre-unlink.sh
index 5112073d6de92..8e02599860ec6 100644
--- a/recipes/r-ngsplot-hg19/pre-unlink.sh
+++ b/recipes/r-ngsplot-hg19/pre-unlink.sh
@@ -1 +1 @@
-ngsplotdb.py remove hg19 > "${PREFIX}/.messages.txt" 2>&1
\ No newline at end of file
+ngsplotdb.py remove hg19 > "${PREFIX}/.messages.txt" 2>&1

From a76b66851420820b81cde8bf03d56687ac9e15f1 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 21:55:39 +0200
Subject: [PATCH 16/31] No need for images in there

---
 recipes/r-ngsplot/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh
index f84c136aa0248..dc83fe21de966 100644
--- a/recipes/r-ngsplot/build.sh
+++ b/recipes/r-ngsplot/build.sh
@@ -2,7 +2,7 @@
 outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 mkdir -p $outdir
 mkdir -p $PREFIX/bin
-cp -R {bin,database,example,galaxy,lib,webings,LICENSE} ${outdir}/
+cp -R {bin,database,example,galaxy,lib,LICENSE} ${outdir}/
 #Set up links for 
 for f in ${outdir}/bin/*; do
     ln -s ${f} ${PREFIX}/bin

From 2a7f5e4be8bd1844635d9eadcdcba2edf03f9ce8 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 22:06:21 +0200
Subject: [PATCH 17/31] Fixing tests

---
 recipes/r-ngsplot/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/r-ngsplot/meta.yaml b/recipes/r-ngsplot/meta.yaml
index e06081f22c04e..d37ab94e9ceb3 100644
--- a/recipes/r-ngsplot/meta.yaml
+++ b/recipes/r-ngsplot/meta.yaml
@@ -25,7 +25,7 @@ requirements:
 
 test:
   commands:
-    - ngsplotdb.py list
+    - ngsplotdb.py list | grep -q "your ngs.plot database may be corrupted."
     - ngs.plot.r | grep -q "Visit https://github.com/shenlab-sinai/ngsplot/wiki/ProgramArguments101 for details"
 
 about:

From 484b1f2a8e6c9c6ac23b6d97a7342028ac791afa Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 22:15:52 +0200
Subject: [PATCH 18/31] Fixing tests

---
 recipes/r-ngsplot/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/r-ngsplot/meta.yaml b/recipes/r-ngsplot/meta.yaml
index d37ab94e9ceb3..78998ce26ac67 100644
--- a/recipes/r-ngsplot/meta.yaml
+++ b/recipes/r-ngsplot/meta.yaml
@@ -25,7 +25,7 @@ requirements:
 
 test:
   commands:
-    - ngsplotdb.py list | grep -q "your ngs.plot database may be corrupted."
+    - ngsplotdb.py list 2>&1 | grep -q "your ngs.plot database may be corrupted."
     - ngs.plot.r | grep -q "Visit https://github.com/shenlab-sinai/ngsplot/wiki/ProgramArguments101 for details"
 
 about:

From e16b59724d33ba82fb0db956771a174d381beb4b Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Wed, 6 Jun 2018 22:25:25 +0200
Subject: [PATCH 19/31] Updated Build Script

---
 recipes/r-ngsplot/build.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh
index dc83fe21de966..4936901cfd560 100644
--- a/recipes/r-ngsplot/build.sh
+++ b/recipes/r-ngsplot/build.sh
@@ -8,3 +8,6 @@ for f in ${outdir}/bin/*; do
     ln -s ${f} ${PREFIX}/bin
     fbname=$(basename "$f")
 done
+
+#Setting environment variable NGSPLOT as requested by authors readme
+export NGSPLOT=${outdir}

From 95efbc3c71d8b420e1034dfca96a7f5666ecfd79 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Fri, 8 Jun 2018 14:17:07 +0200
Subject: [PATCH 20/31] Add Activate / Deactivate scripts for ENV variable

---
 recipes/r-ngsplot/build.sh              | 9 +++++++--
 recipes/r-ngsplot/scripts/activate.sh   | 3 +++
 recipes/r-ngsplot/scripts/deactivate.sh | 4 ++++
 3 files changed, 14 insertions(+), 2 deletions(-)
 create mode 100644 recipes/r-ngsplot/scripts/activate.sh
 create mode 100644 recipes/r-ngsplot/scripts/deactivate.sh

diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh
index 4936901cfd560..2ee37005e3a61 100644
--- a/recipes/r-ngsplot/build.sh
+++ b/recipes/r-ngsplot/build.sh
@@ -9,5 +9,10 @@ for f in ${outdir}/bin/*; do
     fbname=$(basename "$f")
 done
 
-#Setting environment variable NGSPLOT as requested by authors readme
-export NGSPLOT=${outdir}
+#Activate/Deactivate dir
+ACTIVATE_DIR=$PREFIX/etc/conda/activate.d
+DEACTIVATE_DIR=$PREFIX/etc/conda/deactivate.d
+mkdir -p $ACTIVATE_DIR
+mkdir -p $DEACTIVATE_DIR
+cp $RECIPE_DIR/scripts/activate.sh $ACTIVATE_DIR/ngsplot-activate.sh
+cp $RECIPE_DIR/scripts/deactivate.sh $DEACTIVATE_DIR/ngsplot-deactivate.sh
\ No newline at end of file
diff --git a/recipes/r-ngsplot/scripts/activate.sh b/recipes/r-ngsplot/scripts/activate.sh
new file mode 100644
index 0000000000000..6750655473d4e
--- /dev/null
+++ b/recipes/r-ngsplot/scripts/activate.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+export NGSPLOT=$(pwd)/plugins
+export _CONDA_SET_NGSPLOT_ENV=1
diff --git a/recipes/r-ngsplot/scripts/deactivate.sh b/recipes/r-ngsplot/scripts/deactivate.sh
new file mode 100644
index 0000000000000..9dd8e8e66515e
--- /dev/null
+++ b/recipes/r-ngsplot/scripts/deactivate.sh
@@ -0,0 +1,4 @@
+if [[ -n "$_CONDA_SET_NGSPLOT_ENV" ]]; then
+	unset NGSPLOT
+	unset _CONDA_SET_NGSPLOT_ENV
+fi
\ No newline at end of file

From 9c444978c7c817e6cd4af86431a5222642576eb5 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Fri, 8 Jun 2018 14:22:09 +0200
Subject: [PATCH 21/31] Wrong path

---
 recipes/r-ngsplot/scripts/activate.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/r-ngsplot/scripts/activate.sh b/recipes/r-ngsplot/scripts/activate.sh
index 6750655473d4e..56980d78fd8d9 100644
--- a/recipes/r-ngsplot/scripts/activate.sh
+++ b/recipes/r-ngsplot/scripts/activate.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
-export NGSPLOT=$(pwd)/plugins
+export NGSPLOT=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 export _CONDA_SET_NGSPLOT_ENV=1

From b35f91a21ac3ba154cf0e05a7ac7e23d64d164b5 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Fri, 8 Jun 2018 16:00:58 +0200
Subject: [PATCH 22/31] Removing unrequired fbname

---
 recipes/r-ngsplot/build.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh
index 2ee37005e3a61..20bb0f676c984 100644
--- a/recipes/r-ngsplot/build.sh
+++ b/recipes/r-ngsplot/build.sh
@@ -6,7 +6,6 @@ cp -R {bin,database,example,galaxy,lib,LICENSE} ${outdir}/
 #Set up links for 
 for f in ${outdir}/bin/*; do
     ln -s ${f} ${PREFIX}/bin
-    fbname=$(basename "$f")
 done
 
 #Activate/Deactivate dir

From 05101faf04e7b308a9309d242ff37d3699a50827 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Fri, 8 Jun 2018 16:04:32 +0200
Subject: [PATCH 23/31] Add exact name of package

---
 recipes/r-ngsplot/build.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh
index 20bb0f676c984..78190d5f37848 100644
--- a/recipes/r-ngsplot/build.sh
+++ b/recipes/r-ngsplot/build.sh
@@ -13,5 +13,5 @@ ACTIVATE_DIR=$PREFIX/etc/conda/activate.d
 DEACTIVATE_DIR=$PREFIX/etc/conda/deactivate.d
 mkdir -p $ACTIVATE_DIR
 mkdir -p $DEACTIVATE_DIR
-cp $RECIPE_DIR/scripts/activate.sh $ACTIVATE_DIR/ngsplot-activate.sh
-cp $RECIPE_DIR/scripts/deactivate.sh $DEACTIVATE_DIR/ngsplot-deactivate.sh
\ No newline at end of file
+cp $RECIPE_DIR/scripts/activate.sh $ACTIVATE_DIR/${PKG_NAME}-activate.sh
+cp $RECIPE_DIR/scripts/deactivate.sh $DEACTIVATE_DIR/${PKG_NAME}-deactivate.sh
\ No newline at end of file

From 8fb135d8b6aae908b746f3ca75267cd02ec80155 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Fri, 8 Jun 2018 16:05:46 +0200
Subject: [PATCH 24/31] Fixing pipes

---
 recipes/r-ngsplot-hg19/post-link.sh  | 4 ++--
 recipes/r-ngsplot-hg19/pre-unlink.sh | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/post-link.sh b/recipes/r-ngsplot-hg19/post-link.sh
index 6e90b62cd4f35..633457f04f2a8 100644
--- a/recipes/r-ngsplot-hg19/post-link.sh
+++ b/recipes/r-ngsplot-hg19/post-link.sh
@@ -34,11 +34,11 @@ 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
+  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
+ngsplotdb.py install "${TARBALL}" >> "${PREFIX}/.messages.txt" 2>&1
 rm $TARBALL
 rmdir $STAGING
diff --git a/recipes/r-ngsplot-hg19/pre-unlink.sh b/recipes/r-ngsplot-hg19/pre-unlink.sh
index 8e02599860ec6..c7a0f8a7e486d 100644
--- a/recipes/r-ngsplot-hg19/pre-unlink.sh
+++ b/recipes/r-ngsplot-hg19/pre-unlink.sh
@@ -1 +1 @@
-ngsplotdb.py remove hg19 > "${PREFIX}/.messages.txt" 2>&1
+ngsplotdb.py remove hg19 >> "${PREFIX}/.messages.txt" 2>&1

From 30d2a97d1c4cc23981d67feba3cbc5f74d70d483 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Fri, 8 Jun 2018 16:26:04 +0200
Subject: [PATCH 25/31] Get rid of old activate script

---
 recipes/r-ngsplot/scripts/activate.sh | 3 ---
 1 file changed, 3 deletions(-)
 delete mode 100644 recipes/r-ngsplot/scripts/activate.sh

diff --git a/recipes/r-ngsplot/scripts/activate.sh b/recipes/r-ngsplot/scripts/activate.sh
deleted file mode 100644
index 56980d78fd8d9..0000000000000
--- a/recipes/r-ngsplot/scripts/activate.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-export NGSPLOT=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
-export _CONDA_SET_NGSPLOT_ENV=1

From 9b168e62a31ab8bdc9925d2b68add31835cc11a0 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Fri, 8 Jun 2018 16:26:15 +0200
Subject: [PATCH 26/31] Add patch for environment variable in R script

---
 recipes/r-ngsplot/build.sh | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh
index 78190d5f37848..61b519ff5c7c5 100644
--- a/recipes/r-ngsplot/build.sh
+++ b/recipes/r-ngsplot/build.sh
@@ -13,5 +13,13 @@ ACTIVATE_DIR=$PREFIX/etc/conda/activate.d
 DEACTIVATE_DIR=$PREFIX/etc/conda/deactivate.d
 mkdir -p $ACTIVATE_DIR
 mkdir -p $DEACTIVATE_DIR
-cp $RECIPE_DIR/scripts/activate.sh $ACTIVATE_DIR/${PKG_NAME}-activate.sh
-cp $RECIPE_DIR/scripts/deactivate.sh $DEACTIVATE_DIR/${PKG_NAME}-deactivate.sh
\ No newline at end of file
+cp $RECIPE_DIR/scripts/deactivate.sh $DEACTIVATE_DIR/${PKG_NAME}-deactivate.sh
+#Create activate.sh script
+echo > "${ACTIVATE_DIR}/${PKG_NAME}-activate.sh" <<EOF
+#!/bin/bash
+export NGSPLOT="${outdir}"
+export _CONDA_SET_NGSPLOT_ENV=1
+EOF
+
+#Patch ngs.plot.R to use proper path
+sed -i "s#^progpath.*#progpath=$outdir#g" ${outdir}/bin/ngs.plot.r
\ No newline at end of file

From 79777573a56c7df55f5e64bfa414ab75b7ac52a2 Mon Sep 17 00:00:00 2001
From: Marcel Bargull <marcel.bargull@udo.edu>
Date: Sat, 9 Jun 2018 08:37:04 +0200
Subject: [PATCH 27/31] r-ngsplot: patch all scripts, avoid activation script

---
 recipes/r-ngsplot/build.sh              | 26 ++++++++++---------------
 recipes/r-ngsplot/scripts/deactivate.sh |  4 ----
 2 files changed, 10 insertions(+), 20 deletions(-)
 delete mode 100644 recipes/r-ngsplot/scripts/deactivate.sh

diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh
index 61b519ff5c7c5..3ec522d58bca1 100644
--- a/recipes/r-ngsplot/build.sh
+++ b/recipes/r-ngsplot/build.sh
@@ -3,23 +3,17 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 mkdir -p $outdir
 mkdir -p $PREFIX/bin
 cp -R {bin,database,example,galaxy,lib,LICENSE} ${outdir}/
-#Set up links for 
+# Set up links for 
 for f in ${outdir}/bin/*; do
     ln -s ${f} ${PREFIX}/bin
 done
 
-#Activate/Deactivate dir
-ACTIVATE_DIR=$PREFIX/etc/conda/activate.d
-DEACTIVATE_DIR=$PREFIX/etc/conda/deactivate.d
-mkdir -p $ACTIVATE_DIR
-mkdir -p $DEACTIVATE_DIR
-cp $RECIPE_DIR/scripts/deactivate.sh $DEACTIVATE_DIR/${PKG_NAME}-deactivate.sh
-#Create activate.sh script
-echo > "${ACTIVATE_DIR}/${PKG_NAME}-activate.sh" <<EOF
-#!/bin/bash
-export NGSPLOT="${outdir}"
-export _CONDA_SET_NGSPLOT_ENV=1
-EOF
-
-#Patch ngs.plot.R to use proper path
-sed -i "s#^progpath.*#progpath=$outdir#g" ${outdir}/bin/ngs.plot.r
\ No newline at end of file
+# Patch scripts to use proper path and not depend on NGSPLOT env variable
+for f in "${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 "${f}.bak"
+done
diff --git a/recipes/r-ngsplot/scripts/deactivate.sh b/recipes/r-ngsplot/scripts/deactivate.sh
deleted file mode 100644
index 9dd8e8e66515e..0000000000000
--- a/recipes/r-ngsplot/scripts/deactivate.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-if [[ -n "$_CONDA_SET_NGSPLOT_ENV" ]]; then
-	unset NGSPLOT
-	unset _CONDA_SET_NGSPLOT_ENV
-fi
\ No newline at end of file

From a40cf3278b1bc91d9ea18e3545e51bbaf78e984f Mon Sep 17 00:00:00 2001
From: Marcel Bargull <marcel.bargull@udo.edu>
Date: Sat, 9 Jun 2018 18:55:20 +0200
Subject: [PATCH 28/31] r-ngsplot: debugging: show output if test failed

---
 recipes/r-ngsplot-hg19/meta.yaml | 2 +-
 recipes/r-ngsplot/meta.yaml      | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
index f3ca75fc92579..e307901860a15 100644
--- a/recipes/r-ngsplot-hg19/meta.yaml
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -13,7 +13,7 @@ requirements:
     - wget
 test:
   commands:
-    - ngsplotdb.py list | grep "hg19" > "${PREFIX}/.messages.txt" 2>&1
+    - ngsplotdb.py list | grep -qF "hg19" || ngsplotdb.py list
 about:
   home: 'https://github.com/shenlab-sinai/ngsplot'
   license: GPL-2.0
diff --git a/recipes/r-ngsplot/meta.yaml b/recipes/r-ngsplot/meta.yaml
index 78998ce26ac67..6ac386d65d58d 100644
--- a/recipes/r-ngsplot/meta.yaml
+++ b/recipes/r-ngsplot/meta.yaml
@@ -25,8 +25,8 @@ requirements:
 
 test:
   commands:
-    - ngsplotdb.py list 2>&1 | grep -q "your ngs.plot database may be corrupted."
-    - ngs.plot.r | grep -q "Visit https://github.com/shenlab-sinai/ngsplot/wiki/ProgramArguments101 for details"
+    - 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

From f0970689e58e3579a0a20b03c099a0ae9e965810 Mon Sep 17 00:00:00 2001
From: Marcel Bargull <marcel.bargull@udo.edu>
Date: Sat, 9 Jun 2018 19:29:30 +0200
Subject: [PATCH 29/31] r-ngsplot: try || in subshells

---
 recipes/r-ngsplot-hg19/meta.yaml | 2 +-
 recipes/r-ngsplot/meta.yaml      | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
index e307901860a15..f30535e04aa0a 100644
--- a/recipes/r-ngsplot-hg19/meta.yaml
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -13,7 +13,7 @@ requirements:
     - wget
 test:
   commands:
-    - ngsplotdb.py list | grep -qF "hg19" || ngsplotdb.py list
+    - (ngsplotdb.py list | grep -qF "hg19" || ngsplotdb.py list)
 about:
   home: 'https://github.com/shenlab-sinai/ngsplot'
   license: GPL-2.0
diff --git a/recipes/r-ngsplot/meta.yaml b/recipes/r-ngsplot/meta.yaml
index 6ac386d65d58d..cb6afb9bdecb4 100644
--- a/recipes/r-ngsplot/meta.yaml
+++ b/recipes/r-ngsplot/meta.yaml
@@ -25,8 +25,8 @@ requirements:
 
 test:
   commands:
-    - 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
+    - (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

From de5d1a6dc0c4f17fd6fad802e80d219aecabcc62 Mon Sep 17 00:00:00 2001
From: Marcel Bargull <marcel.bargull@udo.edu>
Date: Sat, 9 Jun 2018 19:44:44 +0200
Subject: [PATCH 30/31] r-ngsplot: add missing python dependency

---
 recipes/r-ngsplot/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/r-ngsplot/meta.yaml b/recipes/r-ngsplot/meta.yaml
index cb6afb9bdecb4..051f862e86057 100644
--- a/recipes/r-ngsplot/meta.yaml
+++ b/recipes/r-ngsplot/meta.yaml
@@ -22,6 +22,7 @@ requirements:
     - bioconductor-rsamtools
     - bioconductor-bsgenome
     - bioconductor-shortread
+    - python <3.0a0
 
 test:
   commands:

From 88af4ed923c5cafa77eb10096ad2bb32c79680a9 Mon Sep 17 00:00:00 2001
From: Marcel Bargull <marcel.bargull@udo.edu>
Date: Sat, 9 Jun 2018 20:07:57 +0200
Subject: [PATCH 31/31] r-ngsplot-hg19: fix variable name in post-link.sh

---
 recipes/r-ngsplot-hg19/meta.yaml    | 2 +-
 recipes/r-ngsplot-hg19/post-link.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml
index f30535e04aa0a..da53714010baa 100644
--- a/recipes/r-ngsplot-hg19/meta.yaml
+++ b/recipes/r-ngsplot-hg19/meta.yaml
@@ -8,7 +8,7 @@ build:
   number: 0
 requirements:
   run:
-    - 'r-ngsplot'
+    - r-ngsplot
     - r-base
     - wget
 test:
diff --git a/recipes/r-ngsplot-hg19/post-link.sh b/recipes/r-ngsplot-hg19/post-link.sh
index 633457f04f2a8..dd917be921667 100644
--- a/recipes/r-ngsplot-hg19/post-link.sh
+++ b/recipes/r-ngsplot-hg19/post-link.sh
@@ -3,7 +3,7 @@ FN="ngsplotdb_hg19_75_3.00.tar.gz"
 URLS=(
   "https://drive.google.com/uc?export=download&id=0B5hDZ2BucCI6SURYWW5XdUxnbW8"
 )
-md5="172a6a93de3d1ae8a3ad6d6d79e911f7"
+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