Skip to content

Commit

Permalink
[ci skip] Merge PR 33790
Browse files Browse the repository at this point in the history
Merge PR bioconda#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
Hualin Liu (刘华林) authored Apr 12, 2022
1 parent d74a925 commit 1957d85
Showing 2 changed files with 44 additions and 36 deletions.
7 changes: 7 additions & 0 deletions recipes/pgcgap/build.sh
Original file line number Diff line number Diff line change
@@ -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
73 changes: 37 additions & 36 deletions recipes/pgcgap/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,65 +1,66 @@
{% set name = "pgcgap" %}
{% set version = "1.0.34" %}
{% set version = "1.0.35" %}

package:
name: '{{ name }}'
version: '{{ version }}'

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:

0 comments on commit 1957d85

Please sign in to comment.