From 107b3088ed4760e4332a70f603e1aedb5ad9480a Mon Sep 17 00:00:00 2001
From: Christine Jandrasits <jandrasitsc@rki.de>
Date: Fri, 26 Oct 2018 16:04:40 +0200
Subject: [PATCH 1/3] New version with bugfix and different progressiveMauve
 version.

---
 recipes/seq-seq-pan/meta.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/recipes/seq-seq-pan/meta.yaml b/recipes/seq-seq-pan/meta.yaml
index e5597545f04e8..5c275c617a20a 100644
--- a/recipes/seq-seq-pan/meta.yaml
+++ b/recipes/seq-seq-pan/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.0" %}
+{% set version = "1.0.1" %}
 
 package:
   name: seq-seq-pan
@@ -6,10 +6,10 @@ package:
 
 source:
   url: https://gitlab.com/chrjan/seq-seq-pan/repository/v{{ version }}/archive.tar.gz
-  md5: 7a0c00d8de984f7129c7bcbe4fa26892
+  md5: e053bc23c84493c29926aafafd77c966
 
 build:
-  number: 2
+  number: 1
   skip: True # [osx or py27]
 
 requirements:
@@ -20,7 +20,7 @@ requirements:
     - snakemake ==4.3
     - openjdk
     - argparse
-    - progressivemauve ==snapshot-2015-02-13
+    - mauvealigner ==1.2.0
 
 test:
   commands:

From f65099ca8c0dcd1be433585fda085a9749c437c4 Mon Sep 17 00:00:00 2001
From: Christine Jandrasits <jandrasitsc@rki.de>
Date: Fri, 26 Oct 2018 16:27:15 +0200
Subject: [PATCH 2/3] Keeping old version as folder.

---
 recipes/seq-seq-pan/1.0.0/build.sh  | 16 +++++++++++++
 recipes/seq-seq-pan/1.0.0/meta.yaml | 36 +++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+)
 create mode 100755 recipes/seq-seq-pan/1.0.0/build.sh
 create mode 100644 recipes/seq-seq-pan/1.0.0/meta.yaml

diff --git a/recipes/seq-seq-pan/1.0.0/build.sh b/recipes/seq-seq-pan/1.0.0/build.sh
new file mode 100755
index 0000000000000..b3dabae16b6a1
--- /dev/null
+++ b/recipes/seq-seq-pan/1.0.0/build.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+mkdir -p $PREFIX/bin
+mkdir -p $PREFIX/opt/seq-seq-pan/
+
+
+sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan
+sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan-consensus
+sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan-wga
+sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan-genomedescription
+
+cp -r * $PREFIX/opt/seq-seq-pan/
+ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan $PREFIX/bin
+ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan-consensus $PREFIX/bin
+ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan-wga $PREFIX/bin
+ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan-genomedescription $PREFIX/bin
diff --git a/recipes/seq-seq-pan/1.0.0/meta.yaml b/recipes/seq-seq-pan/1.0.0/meta.yaml
new file mode 100644
index 0000000000000..e5597545f04e8
--- /dev/null
+++ b/recipes/seq-seq-pan/1.0.0/meta.yaml
@@ -0,0 +1,36 @@
+{% set version = "1.0.0" %}
+
+package:
+  name: seq-seq-pan
+  version: {{ version }}
+
+source:
+  url: https://gitlab.com/chrjan/seq-seq-pan/repository/v{{ version }}/archive.tar.gz
+  md5: 7a0c00d8de984f7129c7bcbe4fa26892
+
+build:
+  number: 2
+  skip: True # [osx or py27]
+
+requirements:
+  run:
+    - python
+    - biopython ==1.69
+    - blat ==35
+    - snakemake ==4.3
+    - openjdk
+    - argparse
+    - progressivemauve ==snapshot-2015-02-13
+
+test:
+  commands:
+    - seq-seq-pan -h > /dev/null
+    - seq-seq-pan-wga --no-hooks --config workdir=$PREFIX/opt/seq-seq-pan/example/minimal genomefile=genome_list.txt outfilename=ssp_example -n > /dev/null
+    - java -jar $PREFIX/opt/seq-seq-pan/java/XMFAConsensus/XMFAconsensus_majorityvote.jar -h > /dev/null
+    - seq-seq-pan-consensus -h > /dev/null
+    - seq-seq-pan-genomedescription -h >/dev/null
+
+about:
+  home: https://gitlab.com/chrjan/seq-seq-pan
+  license: FreeBSDLicense
+  summary: seq-seq-pan is a workflow for the SEQuential alignment of SEQuences to build a PAN-genome data structure and a whole-genome-alignment.

From f3cc9a8372da5c92419d7c0856f367fab999520b Mon Sep 17 00:00:00 2001
From: Christine Jandrasits <jandrasitsc@rki.de>
Date: Fri, 26 Oct 2018 16:32:00 +0200
Subject: [PATCH 3/3] Push build number.

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

diff --git a/recipes/seq-seq-pan/meta.yaml b/recipes/seq-seq-pan/meta.yaml
index 5c275c617a20a..dea80b0f6a92f 100644
--- a/recipes/seq-seq-pan/meta.yaml
+++ b/recipes/seq-seq-pan/meta.yaml
@@ -9,7 +9,7 @@ source:
   md5: e053bc23c84493c29926aafafd77c966
 
 build:
-  number: 1
+  number: 2
   skip: True # [osx or py27]
 
 requirements: