From ac93f9ead383b24ebc0299bd83d9b8c4fc21ae25 Mon Sep 17 00:00:00 2001
From: Sang Chul Choi <goshng@yahoo.co.kr>
Date: Thu, 7 Nov 2024 19:55:36 +0900
Subject: [PATCH] Update polap to v0.3.7 Build1 (#51963)
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* Update polap to v0.3.7 Build1

* Update polap to v0.3.7 Build2

* Update polap to v0.3.7 build number upto 1

* Update polap to v0.3.7 build number 2

* Update polap to v0.3.7 build number 3

* Update recipes/polap/meta.yaml

---------

Co-authored-by: Sang Chul Choi <sangchulchoi@sungshin.ac.kr>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/polap/build.sh  | 67 ++++++++++++++++++++++++++++++++++++++---
 recipes/polap/meta.yaml | 36 ++++++++++++----------
 2 files changed, 82 insertions(+), 21 deletions(-)

diff --git a/recipes/polap/build.sh b/recipes/polap/build.sh
index 7a3380a679704..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-ncbitools
+	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-ncbitools
-	run-polap-r-pairs.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 121392e9d8c1a..d24d3aff426e8 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 = "8dd857d8b0a33d692467440c1017beabb171bfde7dae2aa5bd5ebcebd09e70eb" %}
 
 package:
   name: "{{ name }}"
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('polap', max_pin="x.x") }}
 
@@ -20,33 +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
-    - perl-xml-libxml
-    - icu
-    - libxml2
-    - perl
-    - r-base
+    - networkx
+    - pandas
+    - gfatools
+    - 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: