From 1957d85322b18e0137cb931a929d30cdf6479c25 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hualin=20Liu=20=28=E5=88=98=E5=8D=8E=E6=9E=97=29?= Date: Tue, 12 Apr 2022 21:56:43 +0800 Subject: [PATCH] [ci skip] Merge PR 33790 Merge PR #33790, commits were: * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update PGCGAP to v1.0.34 Specified dependency version numbers to spend less memory when performing recipe testing. * update pgcgap build number specify the version of all dependences to occupy less memory * Update build number add dependencies * Merge branch 'master' into pgcgap3 * Merge branch 'bioconda:master' into master * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build-fail-blacklist remove PGCGAP * Update meta.yaml * Merge branch 'master' into pgcgap3 * Merge branch 'bioconda:master' into master * Remove some dependencies to solve error code 137 * Update PGCGAP to v1.0.33 * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/liaochenlanruo/bioconda-recipes * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge branch 'bioconda:master' into master * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes * Merge pull request #3 from bioconda/master Update local * Merge pull request #1 from bioconda/master Update local --- recipes/pgcgap/build.sh | 7 ++++ recipes/pgcgap/meta.yaml | 73 ++++++++++++++++++++-------------------- 2 files changed, 44 insertions(+), 36 deletions(-) diff --git a/recipes/pgcgap/build.sh b/recipes/pgcgap/build.sh index 92795cfd0e5fe..9ac81c03c1519 100644 --- a/recipes/pgcgap/build.sh +++ b/recipes/pgcgap/build.sh @@ -9,6 +9,7 @@ cp Functions/Pan/grep_cds_aas_from_gff3.pl $PREFIX/bin/ cp Functions/COG/COG.pl $PREFIX/bin/ cp Functions/COG/COG2020.pl $PREFIX/bin/ +cp Functions/COG/COGdiamond2022.pl $PREFIX/bin/ cp Functions/COG/get_flag_relative_abundances_table.pl $PREFIX/bin/ cp Functions/COG/Plot_COG.R $PREFIX/bin/ cp Functions/COG/Plot_COG_Abundance.R $PREFIX/bin/ @@ -23,12 +24,16 @@ cp Functions/MASH/Plot_MashHeatmap.R $PREFIX/bin/ cp Functions/Assemble/genome_LenFilter_stats.pl $PREFIX/bin/ cp Functions/Assemble/get_stats_summary.pl $PREFIX/bin/ +cp Functions/ACC/id2seq.pl $PREFIX/bin/ +cp Functions/ACC/get_repeats.pl $PREFIX/bin/ + chmod a+x $PREFIX/bin/pgcgap chmod a+x $PREFIX/bin/plot_3Dpie.R chmod a+x $PREFIX/bin/fmplot.py chmod a+x $PREFIX/bin/grep_cds_aas_from_gff3.pl chmod a+x $PREFIX/bin/COG.pl chmod a+x $PREFIX/bin/COG2020.pl +chmod a+x $PREFIX/bin/COGdiamond2022.pl chmod a+x $PREFIX/bin/get_flag_relative_abundances_table.pl chmod a+x $PREFIX/bin/Plot_COG.R chmod a+x $PREFIX/bin/triangle2list.pl @@ -39,5 +44,7 @@ chmod a+x $PREFIX/bin/get_Mash_Matrix.pl chmod a+x $PREFIX/bin/Plot_MashHeatmap.R chmod a+x $PREFIX/bin/genome_LenFilter_stats.pl chmod a+x $PREFIX/bin/get_stats_summary.pl +chmod a+x $PREFIX/bin/id2seq.pl +chmod a+x $PREFIX/bin/get_repeats.pl pgcgap --version diff --git a/recipes/pgcgap/meta.yaml b/recipes/pgcgap/meta.yaml index e6a9cc3428f5d..9d6678e58b21b 100644 --- a/recipes/pgcgap/meta.yaml +++ b/recipes/pgcgap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pgcgap" %} -{% set version = "1.0.34" %} +{% set version = "1.0.35" %} package: name: '{{ name }}' @@ -7,59 +7,60 @@ package: source: url: https://github.com/liaochenlanruo/pgcgap/archive/v{{ version }}.tar.gz - sha256: ab5373ece8a29262e8f02f5ccdd72262e12dca6381a4139f1164f78d93ef1e25 - + sha256: 533030cba1cad4176493fce05ea5223b5e2c0440ed9c60ad408c97d73119ac4a build: number: 0 - noarch: generic + noarch: generic requirements: host: - perl - - perl-bioperl >=1.6.924 + - perl-bioperl >=1.7.8 - perl-file-tee - perl-file-copy-recursive run: - #- abricate - #- canu - - openjdk - - abyss - - prokka - - mash - #- roary - #- orthofinder - #- fastani - #- fastp - - pal2nal + - abricate =1.0.1 + - abyss =2.3.4 # >=2.3.4 important + - canu =2.1.1 # <2.2 important + - coreutils =9.0 + - fastani =1.33 + - fastp =0.23.2 + - htslib =1.15.1 + - mamba =0.22.1 + - mash =2.3 # + - matplotlib-base =3.5.1 # + - muscle =5.1 # >=5.1 important + - numpy =1.21.5 # + - openjdk # 8.0.112 important +# - java-jdk 8.0.112 # important + - orthofinder =2.5.4 + - panaroo =1.2.10 + - pandas =1.3.5 + - pal2nal =14.1 - perl - - perl-bioperl >=1.6.924 - - perl-file-tee +# - perl-bioperl - perl-data-dumper - - perl-pod-usage - - perl-parallel-forkmanager - perl-file-copy-recursive + - perl-file-tee + - perl-parallel-forkmanager + - perl-pod-usage - perl-posix - - htslib - #- snippy - #- sickle-trim - - r-base + - prokka >=1.14.5 # important +# - python + - r-base >=4.1.1 + - r-corrplot - r-ggplot2 - r-gplots - - r-corrplot - - trimal - - python - - matplotlib-base - - seaborn - - numpy - - pandas - - biopython - r-pheatmap - r-plotrix - #- unicycler - - wget - - coreutils - - mamba + - seaborn =0.11.2 + - sickle-trim =1.33 + - snippy =4.6.0 # >=4.6.0 important + - snpeff =5.0 # 5.1 error important + - trimal =1.4.1 + - unicycler =0.5.0 + - wget =1.20.3 test: commands: