From 22889d6cd1f60665603a140a5fb971235f8abbcd Mon Sep 17 00:00:00 2001
From: Brandon Seah <kbseah@users.noreply.github.com>
Date: Tue, 20 Jun 2023 10:06:54 +0200
Subject: [PATCH] Update short-read-connector to v1.2.0 (#41567)

* Update short-read-connector to v1.2.0

 * Change source URL to GitHub, INRIA server from v1.1.3 not reachable
 * Add C++ compiler dependency for build
 * Main shell script name has changed, update build.sh and tests
 * Use abbreviation for license; add license_family field

* Remove short-read-connector from build blacklist

No longer failing when tested locally

* Change name to match folder; specify license file

* Skip build for OS X

Skip OS X for now because build test failing, see
https://github.com/GATB/short_read_connector/issues/6

---------

Co-authored-by: Silas Kieser <SilasK@users.noreply.github.com>
---
 build-fail-blacklist                   |  3 ---
 recipes/short-read-connector/build.sh  | 21 ++++++++++++++++-----
 recipes/short-read-connector/meta.yaml | 21 ++++++++++++++-------
 3 files changed, 30 insertions(+), 15 deletions(-)

diff --git a/build-fail-blacklist b/build-fail-blacklist
index 456be3cf4a061..3211a284a17d7 100644
--- a/build-fail-blacklist
+++ b/build-fail-blacklist
@@ -578,9 +578,6 @@ recipes/genblasta
 # ImportError: cannot import name 'aveQual'
 recipes/nanosplit
 
-# ../short_read_connector.sh: line 299: /opt/conda/conda-bld/shortreadconnector_1531045819227/work/build/bin/SRC_linker_ram: No such file or directory
-recipes/short-read-connector
-
 # Cpp no such file or dir
 recipes/genepop
 
diff --git a/recipes/short-read-connector/build.sh b/recipes/short-read-connector/build.sh
index 131f802e6d673..922162cf2bb71 100644
--- a/recipes/short-read-connector/build.sh
+++ b/recipes/short-read-connector/build.sh
@@ -7,20 +7,31 @@ sed -i.bak 's/make -j/make -j1/' INSTALL
 sed -i.bak 's/2> log_linker_err//' test/simple_test.sh
 
 # change run_discoSnp++.sh deps path
-sed -i.bak 's|\$EDIR/bin|\$EDIR|' short_read_connector.sh
+sed -i.bak 's|\$EDIR/bin|\$EDIR|' short_read_connector_linker.sh
+sed -i.bak 's|\$EDIR/bin|\$EDIR|' short_read_connector_counter.sh
 
 # remove precompiled binary for dsk
-sed -i.bak 's|\$EDIR/thirdparty/dsk/bin/linux/dsk|dsk|' short_read_connector.sh
-sed -i.bak 's|\$EDIR/thirdparty/dsk/bin/macosx/dsk|dsk|' short_read_connector.sh
+sed -i.bak 's|\$EDIR/thirdparty/dsk/bin/linux/dsk|dsk|' short_read_connector_linker.sh
+sed -i.bak 's|\$EDIR/thirdparty/dsk/bin/macosx/dsk|dsk|' short_read_connector_linker.sh
+# comment out chmod command for precompiled binary for dsk
+sed -i.bak 's/^chmod/# chmod/' short_read_connector_linker.sh
+
+# remove precompiled binary for dsk
+sed -i.bak 's|\$EDIR/thirdparty/dsk/bin/linux/dsk|dsk|' short_read_connector_counter.sh
+sed -i.bak 's|\$EDIR/thirdparty/dsk/bin/macosx/dsk|dsk|' short_read_connector_counter.sh
+# comment out chmod command for precompiled binary for dsk
+sed -i.bak 's/^chmod/# chmod/' short_read_connector_counter.sh
 
 # installation
 sh INSTALL
 
 # copy binaries
-cp short_read_connector.sh ${PREFIX}/bin
+cp short_read_connector_counter.sh ${PREFIX}/bin
+cp short_read_connector_linker.sh ${PREFIX}/bin
 
 # apply permissions for pipeline
-chmod +x ${PREFIX}/bin/short_read_connector.sh
+chmod +x ${PREFIX}/bin/short_read_connector_linker.sh
+chmod +x ${PREFIX}/bin/short_read_connector_counter.sh
 
 # copy external bin
 cp build/bin/* ${PREFIX}/bin
diff --git a/recipes/short-read-connector/meta.yaml b/recipes/short-read-connector/meta.yaml
index 752282aa1c774..b20e32de5f24b 100644
--- a/recipes/short-read-connector/meta.yaml
+++ b/recipes/short-read-connector/meta.yaml
@@ -1,18 +1,20 @@
 package:
-  name: shortreadconnector
-  version: '1.1.3'
+  name: short-read-connector
+  version: '1.2.0'
 
 source:
-  url: "http://gatb-tools.gforge.inria.fr/ci-inria/rconnector-v1.1.3-Source.tar.gz"
-  md5: "dfb9ea38a562df02c5046574d1bba1bb"
+  url: "https://github.com/GATB/short_read_connector/releases/download/v1.2.0/rconnector-v1.2.0-Source.tar.gz"
+  md5: "2b7a3c9bdb5a3d3e2d3c9fdd9b496323"
 
 build:
-  number: 2
+  number: 0
+  skip: True # [osx]
 
 requirements:
   build:
     - make
     - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - cmake
   host:
     - zlib
@@ -22,9 +24,14 @@ requirements:
     - dsk
 test:
   commands:
-    - short_read_connector.sh -h
+    - short_read_connector_linker.sh index -h
+    - short_read_connector_linker.sh query -h
+    - short_read_connector_counter.sh index -h
+    - short_read_connector_counter.sh query -h
 
 about:
   home: https://github.com/GATB/short_read_connector
-  license: GNU Affero General Public License v3.0
+  license: AGPL-3.0
+  license_family: AGPL
+  license_file: LICENSE
   summary: Short read connector enables the comparisons of two read sets