From c5adc5a944c9c478b86ac2c7048807c9c5af6a08 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sun, 14 Jan 2024 15:19:02 -0500
Subject: [PATCH] Update edta to 2.2.0 (#45172)

* Update edta to 2.2.0

* add run_export

* replace tool name

* re-order tools alphabeticaly + add missing tools

* remove tool pins excepted python set to >=3.8

* edit matplotlib to matplotlib-base

* add annosine2

* Update edta to 2.2.0

* edit tests

* edit tests

* softlink EDTA_processI.pl

* I not J

---------

Co-authored-by: Jacques Dainat <jacques.dainat@ird.fr>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/edta/build.sh  |  4 ++-
 recipes/edta/meta.yaml | 61 +++++++++++++++++++++++++++---------------
 2 files changed, 43 insertions(+), 22 deletions(-)

diff --git a/recipes/edta/build.sh b/recipes/edta/build.sh
index 6f788aca9f249..729d94a5a9379 100644
--- a/recipes/edta/build.sh
+++ b/recipes/edta/build.sh
@@ -16,5 +16,7 @@ END
 
 chmod a+x ${PREFIX}/bin/EDTA.pl
 for name in ${EDTA_OTHER_PROGRAMS} ; do
-  ln -s ${PREFIX}/bin/EDTA.pl ${PREFIX}/bin/$(basename $name)
+  ln -sf ${PREFIX}/bin/EDTA.pl ${PREFIX}/bin/$(basename $name)
 done
+
+ln -sf ${EDTA_DIR}/development/EDTA_processI.pl ${PREFIX}/bin/
diff --git a/recipes/edta/meta.yaml b/recipes/edta/meta.yaml
index e9f32040263c3..3e5f7651efd27 100644
--- a/recipes/edta/meta.yaml
+++ b/recipes/edta/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "EDTA" %}
-{% set version = "2.1.0" %}
-{% set sha256 = "d62425df133d7021db57b5b0ecdd38b21ac837c45a8237c0a1ec2da0bd21e6b6" %}
+{% set version = "2.2.0" %}
+{% set sha256 = "3515667804437f749f0bb934812ca83b23ec5472c221786f6e5a0d4b613a1a7a" %}
 
 package:
   name: "{{ name|lower }}"
@@ -11,35 +11,46 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('edta', max_pin='x') }}
 
 requirements:
   run:
-    - perl
+    - annosine2
+    - bedtools
+    - biopython
+    - blast
     - cd-hit
+    - coreutils
+    - genericrepeatfinder
+    - genometools-genometools
+    - glob2
+    - h5py
+    - hmmer
+    - irfinder
+    - keras
+    - ltr_finder
+    - ltr_retriever
     - repeatmodeler
-    - muscle
+    - matplotlib-base
     - mdust
-    - blast
+    - minimap2
+    - multiprocess
+    - muscle
+    - nodejs
     - openjdk
+    - pandas
+    - perl
     - perl-text-soundex
-    - multiprocess
+    - python >=3.8
     - regex
-    - tensorflow ==1.14
-    - keras >=2.2.4
-    - scikit-learn >=0.19.0
-    - biopython
-    - pandas
-    - glob2
-    - h5py <3
-    - python <3.7
+    - scikit-learn
+    - seqtk
+    - swifter
+    - tensorflow
     - tesorter
-    - genericrepeatfinder
-    - genometools-genometools
-    - ltr_retriever
-    - ltr_finder
-    - coreutils
 
 test:
   commands:
@@ -52,7 +63,15 @@ test:
 about:
   home: https://github.com/oushujun/EDTA
   license: GPL-3.0-only
-  license_family: GPL
+  license_family: GPL3
   license_file: LICENSE
   summary: Extensive de-novo TE Annotator
   dev_url: https://github.com/oushujun/EDTA
+  doc_url: https://github.com/oushujun/EDTA/wiki
+
+extra:
+  identifiers:
+    - doi:10.1186/s13059-019-1905-y
+    - doi:10.1101/2022.10.09.511471
+    - biotools:EDTA
+    - usegalaxy-eu:edta