From 8f0ae7c9640c09a6c0f5edee2f8db564016f4231 Mon Sep 17 00:00:00 2001 From: Sang Chul Choi Date: Wed, 6 Nov 2024 20:17:22 +0900 Subject: [PATCH 1/6] Update polap to v0.3.7 Build1 --- recipes/polap/build.sh | 71 +++++++++++++++++++++++++++++++++++++---- recipes/polap/meta.yaml | 8 +++-- 2 files changed, 70 insertions(+), 9 deletions(-) diff --git a/recipes/polap/build.sh b/recipes/polap/build.sh index 343b7d9d0f89f..fd7226afabb7c 100644 --- a/recipes/polap/build.sh +++ b/recipes/polap/build.sh @@ -6,14 +6,72 @@ files=(polap polap-conda-environment-fmlrc.yaml polap-conda-environment.yaml polap-mt.1.c70.3.faa - polap-parsing.sh polap-pt.2.c70.3.faa - polap.sh - run-polap-genes.R - run-polap-jellyfish.R - run-polap-mtcontig.R run-polap-ncbitools - run-polap-pairs.R) + polap-command-completion.sh + polap-constants.sh + polap-function-set-variables.sh + polap-git-hash-version.sh + polap-parsing.sh + polap-test-variables.sh + polap-variables-common.sh + polap-variables-main.sh + polap-variables-mtcontigs.sh + polap-version.sh + run-polap-function-annotate-contig.sh + run-polap-function-annotate.sh + run-polap-function-archive.sh + run-polap-function-assemble.sh + run-polap-function-bioproject.sh + run-polap-function-include.sh + run-polap-function-log.sh + run-polap-function-menus.sh + run-polap-function-miscellaneous.sh + run-polap-function-mtdna.sh + run-polap-function-oga.sh + run-polap-function-polishing.sh + run-polap-function-seeds.sh + run-polap-function-template.sh + run-polap-function-utilities.sh + run-polap-function-wga.sh + run-polap-sh-create-depth-file.sh + run-polap-sh-half-cut.sh + run-polap-sh-minimap2-paf2tab.sh + run-polap-py-find-cc.py + run-polap-py-select-mtdna-2-nx-find-circular-path.py + run-polap-py-select-mtdna-2-nx-simple-cycles.py + run-polap-pairs.R + run-polap-r-assemble-bioproject-3-length-match.R + run-polap-r-blast-mtdna-1-determine-gene.R + run-polap-r-bridge.R + run-polap-r-cc2mtcontig.R + run-polap-r-depth-distribution.R + run-polap-r-depthfilter-gfa.R + run-polap-r-determine-depth-range.R + run-polap-r-determine-depth-range_1.R + run-polap-r-determine-depth-range_2.R + run-polap-r-determine-depth-range_3.R + run-polap-r-determine-depth-range_4.R + run-polap-r-determine-depth-range_5.R + run-polap-r-edges-stats.R + run-polap-r-final-filter-mtcontig.R + run-polap-r-final-mtcontig.R + run-polap-r-final-seed-mtcontig.R + run-polap-r-genes-bed4.R + run-polap-r-genes.R + run-polap-r-get-bioproject-1.R + run-polap-r-jellyfish.R + run-polap-r-mtcontig-contig.R + run-polap-r-mtcontig.R + run-polap-r-pairs.R + run-polap-r-plastid-determine-depth-range.R + run-polap-r-plot-mtdna.R + run-polap-r-prepare-cc.R + run-polap-r-preselect-annotation.R + run-polap-r-select-mtdna-1-nx-gfa-links.R + run-polap-r-template.R + run-polap-r-test-reads-bar-graph.R + polap.sh) for i in "${files[@]}"; do cp src/$i $PREFIX/bin @@ -21,4 +79,3 @@ done chmod +x $PREFIX/bin/polap chmod +x $PREFIX/bin/polap.sh -chmod +x $PREFIX/bin/run-polap-* diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml index eacc9680c84a3..34432e70015f5 100644 --- a/recipes/polap/meta.yaml +++ b/recipes/polap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "polap" %} -{% set version = "0.2.6" %} -{% set sha256 = "6d9b5ffc26ce6feeaa6119d0dda57e07af9e9def55e5510b0ddf237699b15948" %} +{% set version = "0.3.7" %} +{% set sha256 = "e4f65dc0e2a8869057f50f22e7d2acbbde4f6bdb8a75412d3620c468c7108be8" %} package: name: "{{ name }}" @@ -36,6 +36,10 @@ requirements: - assembly-stats - orthofinder - bioconductor-ggtree + - networkx + - pandas + - gfatools + - progressivemauve - perl-xml-libxml - icu - libxml2 From 29d5ddc70901d88ce3972c688c12db706419ec3b Mon Sep 17 00:00:00 2001 From: Sang Chul Choi Date: Thu, 7 Nov 2024 09:47:37 +0900 Subject: [PATCH 2/6] Update polap to v0.3.7 Build2 --- recipes/polap/meta.yaml | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml index 34432e70015f5..43e3e9275fe68 100644 --- a/recipes/polap/meta.yaml +++ b/recipes/polap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "polap" %} {% set version = "0.3.7" %} -{% set sha256 = "e4f65dc0e2a8869057f50f22e7d2acbbde4f6bdb8a75412d3620c468c7108be8" %} +{% set sha256 = "8b4bdc93d7c42705dee93179e93a6f9223779b77f0ec17cf11ac22c6c5dcad5d" %} package: name: "{{ name }}" @@ -20,37 +20,37 @@ requirements: run: - python - flye >=2.9.2 - - seqkit - minimap2 >=2.24 - - blast + - seqkit - bedtools - seqtk - - bioawk - - entrez-direct - - sra-tools - csvtk - - gfastats - kmer-jellyfish - - clustalw + - blast + - entrez-direct + - sra-tools - samtools - - assembly-stats - orthofinder - bioconductor-ggtree - networkx - pandas - gfatools - - progressivemauve - - perl-xml-libxml - - icu - - libxml2 - - perl - - r-base + - r-optparse - r-dplyr - r-readr - - r-optparse - r-stringr - r-tidyr - parallel + - r-base + - bioawk + - assembly-stats + - progressivemauve + - clustalw + - gfastats + - perl-xml-libxml + - icu + - libxml2 + - perl test: commands: From c2ae2add15b1fd6bba5a7cd3bdaf3ccba517ae2a Mon Sep 17 00:00:00 2001 From: Sang Chul Choi Date: Thu, 7 Nov 2024 10:02:42 +0900 Subject: [PATCH 3/6] Update polap to v0.3.7 build number upto 1 --- recipes/polap/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml index 43e3e9275fe68..ac60778118697 100644 --- a/recipes/polap/meta.yaml +++ b/recipes/polap/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('polap', max_pin="x.x") }} From a11ea393eac67aad621df8e1dec12bc71961b4a4 Mon Sep 17 00:00:00 2001 From: Sang Chul Choi Date: Thu, 7 Nov 2024 11:32:30 +0900 Subject: [PATCH 4/6] Update polap to v0.3.7 build number 2 --- recipes/polap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml index ac60778118697..bf33f424005c6 100644 --- a/recipes/polap/meta.yaml +++ b/recipes/polap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "polap" %} {% set version = "0.3.7" %} -{% set sha256 = "8b4bdc93d7c42705dee93179e93a6f9223779b77f0ec17cf11ac22c6c5dcad5d" %} +{% set sha256 = "2039616e78d0df4e02db74dc72198897a3e4ecd72bb738a2bca6b3baf0773975" %} package: name: "{{ name }}" @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 run_exports: - {{ pin_subpackage('polap', max_pin="x.x") }} From 0f471f288d93959dd8a0a396ccb5e7db9b58a6b8 Mon Sep 17 00:00:00 2001 From: Sang Chul Choi Date: Thu, 7 Nov 2024 16:59:15 +0900 Subject: [PATCH 5/6] Update polap to v0.3.7 build number 3 --- recipes/polap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml index bf33f424005c6..fa3a58510d28d 100644 --- a/recipes/polap/meta.yaml +++ b/recipes/polap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "polap" %} {% set version = "0.3.7" %} -{% set sha256 = "2039616e78d0df4e02db74dc72198897a3e4ecd72bb738a2bca6b3baf0773975" %} +{% set sha256 = "8dd857d8b0a33d692467440c1017beabb171bfde7dae2aa5bd5ebcebd09e70eb" %} package: name: "{{ name }}" @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 2 + number: 3 run_exports: - {{ pin_subpackage('polap', max_pin="x.x") }} From 381c4515965a0cc5a55c4eeacafe2d3c0fb6f0f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 7 Nov 2024 11:24:12 +0100 Subject: [PATCH 6/6] Update recipes/polap/meta.yaml --- recipes/polap/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml index fa3a58510d28d..d24d3aff426e8 100644 --- a/recipes/polap/meta.yaml +++ b/recipes/polap/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 3 + number: 1 run_exports: - {{ pin_subpackage('polap', max_pin="x.x") }}