From 061dd53767e094ae7de8ec8c3786d2b1c24f1604 Mon Sep 17 00:00:00 2001
From: Niclas Hofmann <niclas@molgen.mpg.de>
Date: Fri, 20 Sep 2019 09:26:58 +0200
Subject: [PATCH 1/2] cd-hit: be0 conversion and update SRCURL

---
 cd-hit-4.6.1_20120827-0.bee | 83 -------------------------------------
 cd-hit.be0                  | 32 ++++++++++++++
 2 files changed, 32 insertions(+), 83 deletions(-)
 delete mode 100755 cd-hit-4.6.1_20120827-0.bee
 create mode 100755 cd-hit.be0

diff --git a/cd-hit-4.6.1_20120827-0.bee b/cd-hit-4.6.1_20120827-0.bee
deleted file mode 100755
index 47508729b..000000000
--- a/cd-hit-4.6.1_20120827-0.bee
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env beesh
-
-## this file was created by bee init and should be executed to build a
-## bee-package. (Additional hints are located at the end of this file.)
-
-###############################################################################
-## The source URL(s) define the location of the sources that will be
-## downloaded. Version variables may be used to simplify reuse of this bee-file.
-
-SRCURL[0]="https://cdhit.googlecode.com/files/cd-hit-v${PKGVERSION}-2012-08-27.tgz"
-
-###############################################################################
-## Add URLs/pathes to patch files to the PATCHURL array.
-## The sources will be patched in the order of the array.
-
-# PATCHURL+=()
-
-###############################################################################
-## Add filename patterns to the EXCLUDE array of files that should not
-## be added to you package but may be present in the image directory.
-
-# EXCLUDE+=()
-
-###############################################################################
-## Uncomment the next statement, if the software may not be able to be build
-## outside the source directory and need to be build inside the source
-## directory.
-
-# build_in_sourcedir
-
-###############################################################################
-## bee cannot detect buildtypes specified in subdirectories.
-## Sometimes packages "hide" the real sources in a subdirectory named
-## 'src' or 'cmake' or ..
-## use 'sourcesubdir_append' to specify this directory if known.
-
-# sourcesubdir_append src
-
-###############################################################################
-## Change the default (auto-detected) steps to
-## extract, patch, configure/setup, build and install the software.
-## Make sure the mee_install function does install everything to the
-## image directory "${D}"
-
-#mee_extract() {
-#    bee_extract "${@}"
-#}
-
-#mee_patch() {
-#    bee_patch "${@}"
-#}
-
-#mee_configure() {
-#    bee_configure 
-#}
-
-#mee_build() {
-#    bee_build
-#}
-
-mee_install() {
-    start_cmd mkdir -p ${D}${BINDIR}
-    start_cmd make install PREFIX=${D}${BINDIR}
-}
-## by default this may be 'make install DESTDIR="${D}"'
-
-###############################################################################
-##
-## Additional hints:
-##
-## The name of this bee-file should follow the following naming convention:
-##     pkgname-pkgversion-pkgrevision.bee
-##
-## You may remove all comments as long as SRCURL[0]="" is set.
-##
-## Everything in this file will be executed in a bash environment.
-##
-## Build the package by executing
-##     './pkg-version-N.bee' or
-##     'beesh ./pkg-version-N.bee'
-##
-## see http://beezinga.org/
-##
diff --git a/cd-hit.be0 b/cd-hit.be0
new file mode 100755
index 000000000..182b2aa73
--- /dev/null
+++ b/cd-hit.be0
@@ -0,0 +1,32 @@
+#!/usr/bin/env beesh
+
+# BEE_VERSION cd-hit-4.6.1-1
+
+SRCURL[0]="https://github.com/weizhongli/cdhit/archive/V${PKGVERSION}.tar.gz ${PKGNAME}-${PKGVERSION}.tar.gz"
+
+# PATCHURL+=()
+
+# build_in_sourcedir
+
+# sourcesubdir_append src
+
+#mee_extract() {
+#    bee_extract "${@}"
+#}
+
+#mee_patch() {
+#    bee_patch "${@}"
+#}
+
+#mee_configure() {
+#    bee_configure
+#}
+
+#mee_build() {
+#    bee_build
+#}
+
+mee_install() {
+    start_cmd mkdir -p ${D}${BINDIR}
+    start_cmd make install PREFIX=${D}${BINDIR}
+}

From f314fbe5838097f3b0d54cde88e4e149f87b2504 Mon Sep 17 00:00:00 2001
From: Peter Marquardt <wwwutz@molgen.mpg.de>
Date: Tue, 24 Sep 2019 08:19:01 +0200
Subject: [PATCH 2/2] cd-hit: remove

- should live in /package/sequencer
---
 cd-hit.be0 | 32 --------------------------------
 1 file changed, 32 deletions(-)
 delete mode 100755 cd-hit.be0

diff --git a/cd-hit.be0 b/cd-hit.be0
deleted file mode 100755
index 182b2aa73..000000000
--- a/cd-hit.be0
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env beesh
-
-# BEE_VERSION cd-hit-4.6.1-1
-
-SRCURL[0]="https://github.com/weizhongli/cdhit/archive/V${PKGVERSION}.tar.gz ${PKGNAME}-${PKGVERSION}.tar.gz"
-
-# PATCHURL+=()
-
-# build_in_sourcedir
-
-# sourcesubdir_append src
-
-#mee_extract() {
-#    bee_extract "${@}"
-#}
-
-#mee_patch() {
-#    bee_patch "${@}"
-#}
-
-#mee_configure() {
-#    bee_configure
-#}
-
-#mee_build() {
-#    bee_build
-#}
-
-mee_install() {
-    start_cmd mkdir -p ${D}${BINDIR}
-    start_cmd make install PREFIX=${D}${BINDIR}
-}