From 8d737fedf19df51c5e6f94fefa88623ba206064d Mon Sep 17 00:00:00 2001 From: Jean-Francois Pombert Date: Sat, 18 May 2024 18:33:19 -0400 Subject: [PATCH 1/5] perl-text-roman --- recipes/perl-text-roman/build.sh | 25 +++++++++++++++++++++++++ recipes/perl-text-roman/meta.yaml | 25 +++++++++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 recipes/perl-text-roman/build.sh create mode 100644 recipes/perl-text-roman/meta.yaml diff --git a/recipes/perl-text-roman/build.sh b/recipes/perl-text-roman/build.sh new file mode 100644 index 0000000000000..360c94507e0e8 --- /dev/null +++ b/recipes/perl-text-roman/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + ./Build + ./Build test + # Make sure this goes in site + ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. \ No newline at end of file diff --git a/recipes/perl-text-roman/meta.yaml b/recipes/perl-text-roman/meta.yaml new file mode 100644 index 0000000000000..af51b729f2a37 --- /dev/null +++ b/recipes/perl-text-roman/meta.yaml @@ -0,0 +1,25 @@ +package: + name: perl-text-roman + version: "3.5" + +source: + url: https://cpan.metacpan.org/authors/id/S/SY/SYP/Text-Roman-3.5.tar.gz + md5: 1f6b09c0cc1f4425b565ff787a39fd83 + +build: + noarch: generic + number: 2 + +requirements: + build: + - make + host: + - perl + - perl-module-build + run: + - perl + +about: + home: https://metacpan.org/pod/Text::Roman + license: perl_5 + summary: 'converts between arabic and roman numerals' \ No newline at end of file From 80825313506e785e5d4b22d78034fa1eb5cb741b Mon Sep 17 00:00:00 2001 From: Jean-Francois Pombert Date: Thu, 23 May 2024 10:10:09 -0400 Subject: [PATCH 2/5] Update recipes/perl-text-roman/meta.yaml Co-authored-by: Martin Grigorov --- recipes/perl-text-roman/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/perl-text-roman/meta.yaml b/recipes/perl-text-roman/meta.yaml index af51b729f2a37..f20395f9c83b8 100644 --- a/recipes/perl-text-roman/meta.yaml +++ b/recipes/perl-text-roman/meta.yaml @@ -8,7 +8,8 @@ source: build: noarch: generic - number: 2 + number: 0 + run_exports: '{{ pin_subpackage("perl-text-roman", max_pin="x") }}' requirements: build: From 24f9a2b3969415ce4a79171e04faeb6ebdf5d85b Mon Sep 17 00:00:00 2001 From: Jean-Francois Pombert Date: Thu, 23 May 2024 10:10:18 -0400 Subject: [PATCH 3/5] Update recipes/perl-text-roman/meta.yaml Co-authored-by: Martin Grigorov --- recipes/perl-text-roman/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/perl-text-roman/meta.yaml b/recipes/perl-text-roman/meta.yaml index f20395f9c83b8..a9adae683f3d9 100644 --- a/recipes/perl-text-roman/meta.yaml +++ b/recipes/perl-text-roman/meta.yaml @@ -22,5 +22,5 @@ requirements: about: home: https://metacpan.org/pod/Text::Roman - license: perl_5 + license: Artistic-1.0-Perl summary: 'converts between arabic and roman numerals' \ No newline at end of file From a68a8ff39ef0b0b73db361091cf47c178689297f Mon Sep 17 00:00:00 2001 From: Jean-Francois Pombert Date: Thu, 23 May 2024 10:23:02 -0400 Subject: [PATCH 4/5] + test import --- recipes/perl-text-roman/meta.yaml | 4 +++ recipes/syny/build.sh | 32 +++++++++++++++++ recipes/syny/meta.yaml | 58 +++++++++++++++++++++++++++++++ 3 files changed, 94 insertions(+) create mode 100644 recipes/syny/build.sh create mode 100644 recipes/syny/meta.yaml diff --git a/recipes/perl-text-roman/meta.yaml b/recipes/perl-text-roman/meta.yaml index a9adae683f3d9..12c61a7c2e4d3 100644 --- a/recipes/perl-text-roman/meta.yaml +++ b/recipes/perl-text-roman/meta.yaml @@ -20,6 +20,10 @@ requirements: run: - perl +test: + imports: + - Text::Roman + about: home: https://metacpan.org/pod/Text::Roman license: Artistic-1.0-Perl diff --git a/recipes/syny/build.sh b/recipes/syny/build.sh new file mode 100644 index 0000000000000..3b95a0e6bb3cc --- /dev/null +++ b/recipes/syny/build.sh @@ -0,0 +1,32 @@ +#!/bin/sh + +## Moving SYNY to bin subdir +mkdir -p ${PREFIX}/bin +cp -R * ${PREFIX}/bin/ + +##### Circos +# DOWN_DIR=${SRC_DIR}/circos +# mkdir -p ${DOWN_DIR} + +# wget \ +# --no-check-certificate \ +# https://circos.ca/distribution/circos-0.69-9.tgz \ +# -P $DOWN_DIR \ + +# TMP_DIR=${SRC_DIR}/tmp +# mkdir -p ${TMP_DIR} +# tar -zxvf $DOWN_DIR/circos-0.69-9.tgz -C ${TMP_DIR} +# cp -r $TMP_DIR/circos-0.69-9/* ${PREFIX}/ + +##### Text::Roman Perl module +# PERL_LIB=${PREFIX}/perl5 +# mkdir -p ${PERL_LIB} +# wget https://cpan.metacpan.org/authors/id/S/SY/SYP/Text-Roman-3.5.tar.gz -P ${SRC_DIR} +# tar -zxvf ${SRC_DIR}/Text-Roman-3.5.tar.gz -C ${PERL_LIB} +# mv ${PERL_LIB}/Text-Roman-3.5/lib/* ${PERL_LIB} +# rm -R ${PERL_LIB}/Text-Roman-3.5* + +# mkdir -p ${PREFIX}/etc/conda/activate.d +# cat <> ${PREFIX}/etc/conda/activate.d/syny.sh +# export PERL5LIB=$PERL5LIB:$PERL_LIB +# EOF \ No newline at end of file diff --git a/recipes/syny/meta.yaml b/recipes/syny/meta.yaml new file mode 100644 index 0000000000000..d88134248a1ad --- /dev/null +++ b/recipes/syny/meta.yaml @@ -0,0 +1,58 @@ +{% set name = "syny" %} +{% set version = "1.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/PombertLab/SYNY/archive/refs/tags/{{ version }}.tar.gz + md5: 2bb708ff3eac4c499e2450eaa863d771 + +requirements: + host: + - perl + - python + run: + - perl + - python + - matplotlib + - pandas + - seaborn + - scipy + - libgd + - perl-perlio-gzip + - perl-getopt-argvfile + - perl-clone + - perl-config-general + - perl-font-ttf + - perl-list-moreutils + - perl-math-bezier + - perl-math-round + - perl-math-vecstat + - perl-params-validate + - perl-readonly + - perl-regexp-common + - perl-set-intspan + - perl-statistics-basic + - perl-SVG + - perl-text-format + - perl-gd + - perl-text-roman + - minimap2>=2.28 + - mashmap>=3.1.3 + - diamond>=2.1.9 + - circos + +about: + home: https://github.com/PombertLab/SYNY + license: MIT + summary: "Genome collinearity inferences" + +test: + commands: + - run_syny.pl -h + +extra: + recipe-maintainers: + - Pombert-JF From c2c2da4bb941a4d069b04bc95aa216c967c41d98 Mon Sep 17 00:00:00 2001 From: Jean-Francois Pombert Date: Thu, 23 May 2024 10:27:30 -0400 Subject: [PATCH 5/5] Delete recipes/syny directory --- recipes/syny/build.sh | 32 ----------------------- recipes/syny/meta.yaml | 58 ------------------------------------------ 2 files changed, 90 deletions(-) delete mode 100644 recipes/syny/build.sh delete mode 100644 recipes/syny/meta.yaml diff --git a/recipes/syny/build.sh b/recipes/syny/build.sh deleted file mode 100644 index 3b95a0e6bb3cc..0000000000000 --- a/recipes/syny/build.sh +++ /dev/null @@ -1,32 +0,0 @@ -#!/bin/sh - -## Moving SYNY to bin subdir -mkdir -p ${PREFIX}/bin -cp -R * ${PREFIX}/bin/ - -##### Circos -# DOWN_DIR=${SRC_DIR}/circos -# mkdir -p ${DOWN_DIR} - -# wget \ -# --no-check-certificate \ -# https://circos.ca/distribution/circos-0.69-9.tgz \ -# -P $DOWN_DIR \ - -# TMP_DIR=${SRC_DIR}/tmp -# mkdir -p ${TMP_DIR} -# tar -zxvf $DOWN_DIR/circos-0.69-9.tgz -C ${TMP_DIR} -# cp -r $TMP_DIR/circos-0.69-9/* ${PREFIX}/ - -##### Text::Roman Perl module -# PERL_LIB=${PREFIX}/perl5 -# mkdir -p ${PERL_LIB} -# wget https://cpan.metacpan.org/authors/id/S/SY/SYP/Text-Roman-3.5.tar.gz -P ${SRC_DIR} -# tar -zxvf ${SRC_DIR}/Text-Roman-3.5.tar.gz -C ${PERL_LIB} -# mv ${PERL_LIB}/Text-Roman-3.5/lib/* ${PERL_LIB} -# rm -R ${PERL_LIB}/Text-Roman-3.5* - -# mkdir -p ${PREFIX}/etc/conda/activate.d -# cat <> ${PREFIX}/etc/conda/activate.d/syny.sh -# export PERL5LIB=$PERL5LIB:$PERL_LIB -# EOF \ No newline at end of file diff --git a/recipes/syny/meta.yaml b/recipes/syny/meta.yaml deleted file mode 100644 index d88134248a1ad..0000000000000 --- a/recipes/syny/meta.yaml +++ /dev/null @@ -1,58 +0,0 @@ -{% set name = "syny" %} -{% set version = "1.1" %} - -package: - name: "{{ name|lower }}" - version: "{{ version }}" - -source: - url: https://github.com/PombertLab/SYNY/archive/refs/tags/{{ version }}.tar.gz - md5: 2bb708ff3eac4c499e2450eaa863d771 - -requirements: - host: - - perl - - python - run: - - perl - - python - - matplotlib - - pandas - - seaborn - - scipy - - libgd - - perl-perlio-gzip - - perl-getopt-argvfile - - perl-clone - - perl-config-general - - perl-font-ttf - - perl-list-moreutils - - perl-math-bezier - - perl-math-round - - perl-math-vecstat - - perl-params-validate - - perl-readonly - - perl-regexp-common - - perl-set-intspan - - perl-statistics-basic - - perl-SVG - - perl-text-format - - perl-gd - - perl-text-roman - - minimap2>=2.28 - - mashmap>=3.1.3 - - diamond>=2.1.9 - - circos - -about: - home: https://github.com/PombertLab/SYNY - license: MIT - summary: "Genome collinearity inferences" - -test: - commands: - - run_syny.pl -h - -extra: - recipe-maintainers: - - Pombert-JF