From 55adf8ac136b778ec307ac35be5afa6b47e11514 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Mon, 4 Feb 2019 00:17:37 +0100 Subject: [PATCH 1/4] Update pinnings for clustalw, hmmer, pybedtools and t_coffee --- build-fail-blacklist | 3 +++ recipes/clustalw/meta.yaml | 2 +- recipes/hmmer/meta.yaml | 2 +- recipes/pybedtools/0.6.9/meta.yaml | 2 +- recipes/pybedtools/meta.yaml | 2 +- recipes/t_coffee/meta.yaml | 2 +- 6 files changed, 8 insertions(+), 5 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 995eabd6756e3..79a87cd4c341f 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1,3 +1,6 @@ +# Unclear that the following old versions are still needed +recipes/hmmer/2.3.2 + # The build string needs to be modified to account for the [nocairo] feature recipes/genometools-genometools/1.5.10-nocairo diff --git a/recipes/clustalw/meta.yaml b/recipes/clustalw/meta.yaml index f15b3361a9a6d..e42ee9a7bfa6e 100644 --- a/recipes/clustalw/meta.yaml +++ b/recipes/clustalw/meta.yaml @@ -8,7 +8,7 @@ package: version: 2.1 build: - number: 2 + number: 3 skip: False source: diff --git a/recipes/hmmer/meta.yaml b/recipes/hmmer/meta.yaml index e6d8188d36464..9b24a05e73c5e 100644 --- a/recipes/hmmer/meta.yaml +++ b/recipes/hmmer/meta.yaml @@ -7,7 +7,7 @@ source: sha256: a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/pybedtools/0.6.9/meta.yaml b/recipes/pybedtools/0.6.9/meta.yaml index 29321a936679d..bc46a8627eb44 100644 --- a/recipes/pybedtools/0.6.9/meta.yaml +++ b/recipes/pybedtools/0.6.9/meta.yaml @@ -7,7 +7,7 @@ source: md5: a24e4bcd0c89beb9535295db964f6a4a build: - number: 2 + number: 3 skip: True # [py3k] requirements: diff --git a/recipes/pybedtools/meta.yaml b/recipes/pybedtools/meta.yaml index 28fdb83d3b66e..475cfc04d3e53 100644 --- a/recipes/pybedtools/meta.yaml +++ b/recipes/pybedtools/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 4eebd2cd1764ee1c604fd881703c3e329195485350b987b7fb8db42d232984f6 build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/t_coffee/meta.yaml b/recipes/t_coffee/meta.yaml index 1f05f3b6bcc80..e56557557c8a1 100644 --- a/recipes/t_coffee/meta.yaml +++ b/recipes/t_coffee/meta.yaml @@ -8,7 +8,7 @@ source: build: skip: True # [osx] - number: 7 + number: 8 entry_points: - t_coffee = t_coffee.__main__:main From 1c198c02ca23411b3aea100061f66ecef444eab5 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Mon, 4 Feb 2019 00:49:19 +0100 Subject: [PATCH 2/4] Update recipes --- recipes/pybedtools/0.6.9/meta.yaml | 2 +- recipes/pybedtools/meta.yaml | 2 +- recipes/t_coffee/meta.yaml | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pybedtools/0.6.9/meta.yaml b/recipes/pybedtools/0.6.9/meta.yaml index bc46a8627eb44..5a4a02e278b1a 100644 --- a/recipes/pybedtools/0.6.9/meta.yaml +++ b/recipes/pybedtools/0.6.9/meta.yaml @@ -12,7 +12,7 @@ build: requirements: build: - - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - python - six diff --git a/recipes/pybedtools/meta.yaml b/recipes/pybedtools/meta.yaml index 475cfc04d3e53..70002b7265559 100644 --- a/recipes/pybedtools/meta.yaml +++ b/recipes/pybedtools/meta.yaml @@ -11,7 +11,7 @@ build: requirements: build: - - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - python - six diff --git a/recipes/t_coffee/meta.yaml b/recipes/t_coffee/meta.yaml index e56557557c8a1..9a553f032ccd1 100644 --- a/recipes/t_coffee/meta.yaml +++ b/recipes/t_coffee/meta.yaml @@ -3,8 +3,8 @@ package: version: "11.0.8" source: - url: http://www.tcoffee.org/Packages/Stable/Latest/linux/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.bin - md5: 2e375405c9ebb977adf87c145ca698bb + url: http://www.tcoffee.org/Packages/Beta/Version_11.00.8b3dfb8/T-COFFEE_installer_Version_11.00.8b3dfb8_linux_x64.bin + md5: 9bc85b1fa201181c16815c9077d6fd8b build: skip: True # [osx] From 1f65e6a505c795ab57cda92a2bb8d2cb85c042db Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Mon, 4 Feb 2019 08:54:49 +0100 Subject: [PATCH 3/4] hashy hash --- recipes/t_coffee/build.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/t_coffee/build.sh b/recipes/t_coffee/build.sh index c15db3147c3c1..e7da36ca98ff0 100755 --- a/recipes/t_coffee/build.sh +++ b/recipes/t_coffee/build.sh @@ -6,8 +6,8 @@ export LDFLAGS="-L$PREFIX/lib" TCOFFEE_FOLDER_NAME="${PKG_NAME}-${PKG_VERSION}" TCOFFEE_INSTALL_PATH="$PREFIX/lib/$TCOFFEE_FOLDER_NAME" -chmod +x T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.bin -./T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.bin \ +chmod +x T-COFFEE_installer_Version_11.00.8b3dfb8_linux_x64.bin +./T-COFFEE_installer_Version_11.00.8b3dfb8_linux_x64.bin \ --prefix "$TCOFFEE_INSTALL_PATH" \ --mode unattended \ --user_email username@hostname.com From 0cbc6d74cf793f311000292c86ab200d5e6b82a9 Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Mon, 4 Feb 2019 10:43:07 +0100 Subject: [PATCH 4/4] t_coffee needs quite a bit of TLC, skip until later --- recipes/t_coffee/build.sh | 4 ++-- recipes/t_coffee/meta.yaml | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/t_coffee/build.sh b/recipes/t_coffee/build.sh index e7da36ca98ff0..c15db3147c3c1 100755 --- a/recipes/t_coffee/build.sh +++ b/recipes/t_coffee/build.sh @@ -6,8 +6,8 @@ export LDFLAGS="-L$PREFIX/lib" TCOFFEE_FOLDER_NAME="${PKG_NAME}-${PKG_VERSION}" TCOFFEE_INSTALL_PATH="$PREFIX/lib/$TCOFFEE_FOLDER_NAME" -chmod +x T-COFFEE_installer_Version_11.00.8b3dfb8_linux_x64.bin -./T-COFFEE_installer_Version_11.00.8b3dfb8_linux_x64.bin \ +chmod +x T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.bin +./T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.bin \ --prefix "$TCOFFEE_INSTALL_PATH" \ --mode unattended \ --user_email username@hostname.com diff --git a/recipes/t_coffee/meta.yaml b/recipes/t_coffee/meta.yaml index 9a553f032ccd1..1f05f3b6bcc80 100644 --- a/recipes/t_coffee/meta.yaml +++ b/recipes/t_coffee/meta.yaml @@ -3,12 +3,12 @@ package: version: "11.0.8" source: - url: http://www.tcoffee.org/Packages/Beta/Version_11.00.8b3dfb8/T-COFFEE_installer_Version_11.00.8b3dfb8_linux_x64.bin - md5: 9bc85b1fa201181c16815c9077d6fd8b + url: http://www.tcoffee.org/Packages/Stable/Latest/linux/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.bin + md5: 2e375405c9ebb977adf87c145ca698bb build: skip: True # [osx] - number: 8 + number: 7 entry_points: - t_coffee = t_coffee.__main__:main