From 8ff150fa0dec441e8b041188761c4615984a9980 Mon Sep 17 00:00:00 2001 From: entzian Date: Mon, 4 Feb 2019 15:35:38 +0100 Subject: [PATCH 01/24] build script --- recipes/pourRNA/build.sh | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 recipes/pourRNA/build.sh diff --git a/recipes/pourRNA/build.sh b/recipes/pourRNA/build.sh new file mode 100644 index 0000000000000..a333699b536d3 --- /dev/null +++ b/recipes/pourRNA/build.sh @@ -0,0 +1,6 @@ +#!/bin/sh + +autoreconf -i +./configure +make +make install From 43ae77065ac864dfbff3de7babcc018b47caebe2 Mon Sep 17 00:00:00 2001 From: entzian Date: Mon, 4 Feb 2019 19:41:58 +0100 Subject: [PATCH 02/24] Create meta.yaml --- recipes/pourRNA/meta.yaml | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 recipes/pourRNA/meta.yaml diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml new file mode 100644 index 0000000000000..68997b434426c --- /dev/null +++ b/recipes/pourRNA/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "pourRNA" %} +{% set version = "1.0.0" %} +{% set sha256 = "b72106c44c3bc752b9e53ea564f41d70107ea9349fe536f5570be8cdf59fae70" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/ViennaRNA/pourRNA/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - {{ compiler('cxx') }} + - autoconf + - automake + host: + - gengetopt + - viennarna + run: + - viennarna + +test: + commands: + - pourRNA --version + +about: + home: https://github.com/ViennaRNA/pourRNA/ + license: GPL + license_file: COPYING +summary: "Compute local minima and energy barriers of a landscape." From 4b617afc935730f443f23f281a4fbaca9093a79c Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Mon, 4 Feb 2019 20:38:52 +0100 Subject: [PATCH 03/24] lowercase name --- recipes/pourRNA/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index 68997b434426c..24ab120c2efaf 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -1,4 +1,4 @@ -{% set name = "pourRNA" %} +{% set name = "pourrna" %} {% set version = "1.0.0" %} {% set sha256 = "b72106c44c3bc752b9e53ea564f41d70107ea9349fe536f5570be8cdf59fae70" %} From 2c3fed809ed8a21a6980921e93d145cbb1bbffae Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Mon, 4 Feb 2019 20:48:11 +0100 Subject: [PATCH 04/24] add about:summary --- recipes/pourRNA/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index 24ab120c2efaf..bea56d4a2f9f9 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -32,4 +32,4 @@ about: home: https://github.com/ViennaRNA/pourRNA/ license: GPL license_file: COPYING -summary: "Compute local minima and energy barriers of a landscape." + summary: "Compute local minima and energy barriers of a landscape." From a1076c082e4ec893ca3ab8e85d7ec0caba7625e7 Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 11:33:42 +0100 Subject: [PATCH 05/24] rebuild viennarna --- recipes/viennarna/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/viennarna/meta.yaml b/recipes/viennarna/meta.yaml index 8af20366790d1..d99a5bb0f0569 100644 --- a/recipes/viennarna/meta.yaml +++ b/recipes/viennarna/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: url: https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-{{ version }}.tar.gz From 65a936ce6b75d535cb6a5d3da866886b062acb4f Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 12:20:02 +0100 Subject: [PATCH 06/24] test libstdcxx-ng --- recipes/pourRNA/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index bea56d4a2f9f9..a51e0a2eb5526 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -23,7 +23,7 @@ requirements: - viennarna run: - viennarna - + - libstdcxx-ng test: commands: - pourRNA --version From 1c26a4203b03e27ef012ef01ffd2afe7f75e1ff3 Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 12:44:26 +0100 Subject: [PATCH 07/24] Revert "rebuild viennarna" This reverts commit a1076c082e4ec893ca3ab8e85d7ec0caba7625e7. --- recipes/viennarna/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/viennarna/meta.yaml b/recipes/viennarna/meta.yaml index d99a5bb0f0569..8af20366790d1 100644 --- a/recipes/viennarna/meta.yaml +++ b/recipes/viennarna/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 0 source: url: https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-{{ version }}.tar.gz From 6bf21122e0b6c92836af6348f2b2d7c9555e00ac Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 12:58:52 +0100 Subject: [PATCH 08/24] libstc++ with c++11 support --- recipes/pourRNA/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index a51e0a2eb5526..9c6a928c51fe6 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -16,14 +16,16 @@ build: requirements: build: - {{ compiler('cxx') }} + - libstdcxx-ng >=6.0.18 - autoconf - automake host: + - libstdcxx-ng >=6.0.18 - gengetopt - viennarna run: + - libstdcxx-ng >=6.0.18 - viennarna - - libstdcxx-ng test: commands: - pourRNA --version From 32e71aa3d9cd79dff06cb23f9a238d48960f8f2d Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 13:16:08 +0100 Subject: [PATCH 09/24] + old lib --- recipes/pourRNA/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index 9c6a928c51fe6..5c12c4c196cb2 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -25,6 +25,7 @@ requirements: - viennarna run: - libstdcxx-ng >=6.0.18 + - libstdcxx-ng 6.0.0 - viennarna test: commands: From 1bfb7bcca2052eb9c7ee5f89e8e6ba2d6bc9b96d Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 13:42:50 +0100 Subject: [PATCH 10/24] test --- recipes/pourRNA/meta.yaml | 1 - recipes/viennarna/meta.yaml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index 5c12c4c196cb2..9c6a928c51fe6 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -25,7 +25,6 @@ requirements: - viennarna run: - libstdcxx-ng >=6.0.18 - - libstdcxx-ng 6.0.0 - viennarna test: commands: diff --git a/recipes/viennarna/meta.yaml b/recipes/viennarna/meta.yaml index 8af20366790d1..d99a5bb0f0569 100644 --- a/recipes/viennarna/meta.yaml +++ b/recipes/viennarna/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: url: https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-{{ version }}.tar.gz From a602623c051862c642f3a4133a093c44b88fb2ef Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 14:23:12 +0100 Subject: [PATCH 11/24] test2 --- recipes/pourRNA/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index 9c6a928c51fe6..ed5dc02c864d2 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -16,15 +16,15 @@ build: requirements: build: - {{ compiler('cxx') }} - - libstdcxx-ng >=6.0.18 + - libstdcxx-ng >=6.0.18 - autoconf - automake host: - - libstdcxx-ng >=6.0.18 + - libstdcxx-ng >=6.0.18 - gengetopt - viennarna run: - - libstdcxx-ng >=6.0.18 + - libstdc++6 - viennarna test: commands: From 0762020fa1391d10f7134c9e61ec80c7a5a06ee7 Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 14:24:48 +0100 Subject: [PATCH 12/24] build 0 --- recipes/viennarna/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/viennarna/meta.yaml b/recipes/viennarna/meta.yaml index d99a5bb0f0569..8af20366790d1 100644 --- a/recipes/viennarna/meta.yaml +++ b/recipes/viennarna/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 0 source: url: https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-{{ version }}.tar.gz From daed246abde8afef673dbaf4d8d0e8a918576f19 Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 14:52:49 +0100 Subject: [PATCH 13/24] without automake --- recipes/pourRNA/meta.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index ed5dc02c864d2..0d099e019582c 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -16,15 +16,10 @@ build: requirements: build: - {{ compiler('cxx') }} - - libstdcxx-ng >=6.0.18 - - autoconf - - automake host: - - libstdcxx-ng >=6.0.18 - gengetopt - viennarna run: - - libstdc++6 - viennarna test: commands: From 37a81f3b5974a501b9ee9d4818be0dc4fd99819d Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 15:06:13 +0100 Subject: [PATCH 14/24] without autoreconf --- recipes/pourRNA/build.sh | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/pourRNA/build.sh b/recipes/pourRNA/build.sh index a333699b536d3..ace9b2ef0043c 100644 --- a/recipes/pourRNA/build.sh +++ b/recipes/pourRNA/build.sh @@ -1,6 +1,5 @@ #!/bin/sh -autoreconf -i ./configure make make install From aa8c8f4f75051b9ab69a459d1a4770333770c7ee Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 15:19:39 +0100 Subject: [PATCH 15/24] url update --- recipes/pourRNA/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index 0d099e019582c..b6ecd56aca54d 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -1,13 +1,13 @@ {% set name = "pourrna" %} {% set version = "1.0.0" %} -{% set sha256 = "b72106c44c3bc752b9e53ea564f41d70107ea9349fe536f5570be8cdf59fae70" %} +{% set sha256 = "099b29093a1385ab4a4f454d34e27c463ff73864b5e827ee982fc5398723a68c" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/ViennaRNA/pourRNA/archive/v{{ version }}.tar.gz + url: https://github.com/ViennaRNA/pourRNA/releases/download/v{{ version }}/pourRNA-{{ version }}.tar.gz sha256: {{ sha256 }} build: From b9d504221b07f663f76f55f14d0d4cf4b5cc3316 Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 15:46:09 +0100 Subject: [PATCH 16/24] test --- recipes/pourRNA/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index b6ecd56aca54d..b7de565a87bca 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -30,3 +30,4 @@ about: license: GPL license_file: COPYING summary: "Compute local minima and energy barriers of a landscape." + From 2e0622df56f99d7f7437138cf027b5f05e202be7 Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 15:55:59 +0100 Subject: [PATCH 17/24] key --- recipes/pourRNA/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index b7de565a87bca..e81aa052c668f 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pourrna" %} {% set version = "1.0.0" %} -{% set sha256 = "099b29093a1385ab4a4f454d34e27c463ff73864b5e827ee982fc5398723a68c" %} +{% set sha256 = "ea6fddbc8bda67b2a55b8b758d4b511321c911b5c12dc005410055650fb6132e" %} package: name: {{ name }} From a0522eb2ffd5678a48389d91ed3f4a67d79517a3 Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 16:35:35 +0100 Subject: [PATCH 18/24] with prefix --- recipes/pourRNA/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pourRNA/build.sh b/recipes/pourRNA/build.sh index ace9b2ef0043c..a8a60ca215f35 100644 --- a/recipes/pourRNA/build.sh +++ b/recipes/pourRNA/build.sh @@ -1,5 +1,5 @@ #!/bin/sh -./configure +./configure --prefix=$PREFIX make make install From eb29bf006193604401011c57badc75fb2a505b7f Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Tue, 5 Feb 2019 23:53:06 +0100 Subject: [PATCH 19/24] v1.0.1 --- recipes/pourRNA/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index e81aa052c668f..613974c309f90 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pourrna" %} -{% set version = "1.0.0" %} -{% set sha256 = "ea6fddbc8bda67b2a55b8b758d4b511321c911b5c12dc005410055650fb6132e" %} +{% set version = "1.0.1" %} +{% set sha256 = "62635d3777403865a2801c78e42569abb232bc6a79abe34419ad4bf3c0701b0e" %} package: name: {{ name }} From 51e873c325d4b04d86147dc9318469fe372dcc30 Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Thu, 7 Feb 2019 10:10:11 +0100 Subject: [PATCH 20/24] + prefix --- recipes/pourRNA/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pourRNA/build.sh b/recipes/pourRNA/build.sh index a8a60ca215f35..e2485e82e9cfd 100644 --- a/recipes/pourRNA/build.sh +++ b/recipes/pourRNA/build.sh @@ -1,5 +1,5 @@ #!/bin/sh -./configure --prefix=$PREFIX +./configure --prefix="${PREFIX}" make make install From abdb42789f58c80b686d4271927f06e77c67af9d Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Thu, 7 Feb 2019 10:10:52 +0100 Subject: [PATCH 21/24] GPLv2 --- recipes/pourRNA/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index 613974c309f90..70510dabc1d99 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -27,7 +27,7 @@ test: about: home: https://github.com/ViennaRNA/pourRNA/ - license: GPL + license: GPLv2 license_file: COPYING summary: "Compute local minima and energy barriers of a landscape." From bf75cda11ba4f622ff079ab6c9d82cc1676e852b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 7 Feb 2019 10:34:41 +0100 Subject: [PATCH 22/24] add `make check` Thanks for the hint @eggzilla --- recipes/pourRNA/build.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/pourRNA/build.sh b/recipes/pourRNA/build.sh index e2485e82e9cfd..305d19aeaddac 100644 --- a/recipes/pourRNA/build.sh +++ b/recipes/pourRNA/build.sh @@ -3,3 +3,4 @@ ./configure --prefix="${PREFIX}" make make install +make check From 79a603264f817c54f8dc240532589a6298d7e2b7 Mon Sep 17 00:00:00 2001 From: Gregor Entzian Date: Fri, 8 Feb 2019 10:18:52 +0100 Subject: [PATCH 23/24] pin to viennarna < 3 --- recipes/pourRNA/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index 70510dabc1d99..f1aa4c9d476b8 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -18,9 +18,9 @@ requirements: - {{ compiler('cxx') }} host: - gengetopt - - viennarna + - viennarna >=2.4.11,<3.0.0 run: - - viennarna + - viennarna >=2.4.11,<3.0.0 test: commands: - pourRNA --version From afa7cafb38f70919267246bb5727155193e4f270 Mon Sep 17 00:00:00 2001 From: Martin Raden Date: Fri, 8 Feb 2019 14:38:50 +0100 Subject: [PATCH 24/24] summary extended --- recipes/pourRNA/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pourRNA/meta.yaml b/recipes/pourRNA/meta.yaml index f1aa4c9d476b8..e7d143b9a62d9 100644 --- a/recipes/pourRNA/meta.yaml +++ b/recipes/pourRNA/meta.yaml @@ -29,5 +29,5 @@ about: home: https://github.com/ViennaRNA/pourRNA/ license: GPLv2 license_file: COPYING - summary: "Compute local minima and energy barriers of a landscape." + summary: "Compute local minima and respective transition rates of an RNA energy landscape."