Update Edta 2.2.2 - fix path to LTR_FINDER_PARALLEL (#52404)

* pin ltr_retriever version >=3.0.0

* remove LTR_FINDER_PARALLEL from EDTA as it has to come from conda installation

* remove pin ltr_retriever

* re put the pin to ltr_retriever

* re set the LTR_FINDER_parallel stuff from EDTA

* remove LTR pin. SHould compile because recipe identical as the one made last week

* remove LTR_FINDER_PARALLEL_DIR coming from EDTA

* try again to pin ltr_retriever >=3.0.0

* add repeatmasker=4.1.2.p1

* fix pin

* remove repeatmasker pin

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <[email protected]>

recipes/edta/build.sh

@@ -18,12 +18,3 @@ chmod a+x ${PREFIX}/bin/EDTA.pl
 for name in ${EDTA_OTHER_PROGRAMS} ; do
   ln -sf ${PREFIX}/bin/EDTA.pl ${PREFIX}/bin/$(basename $name)
 done
-
-LTR_FINDER_PARALLEL_DIR=${EDTA_DIR}/bin/LTR_FINDER_parallel
-
-cat <<END >>${PREFIX}/bin/LTR_FINDER_parallel
-#!/bin/bash
-perl ${LTR_FINDER_PARALLEL_DIR}/LTR_FINDER_parallel \$@
-END
-
-chmod a+x ${PREFIX}/bin/LTR_FINDER_parallel

recipes/edta/meta.yaml

@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   noarch: generic
   run_exports:
     - {{ pin_subpackage('edta', max_pin='x') }}
@@ -28,7 +28,7 @@ requirements:
     - helitronscanner
     - ltr_finder_parallel
     - ltr_harvest_parallel
-    - ltr_retriever
+    - ltr_retriever >=3.0.0
     - mdust
     - muscle
     - openjdk
@@ -38,12 +38,13 @@ requirements:
     - perl-text-soundex
     - python >=3.8
     - pyarrow
-    - r-base 
-    - r-dplyr 
-    - r-ggplot2 
+    - r-base
+    - r-dplyr
+    - r-ggplot2
     - r-here
-    - r-tidyr 
-    - repeatmodeler
+    - r-tidyr
+    - repeatmodeler >=2
+    - repeatmasker
     - samtools
     - tesorter
     - tir-learner
@@ -57,13 +58,13 @@ test:
     - lib-test.pl -h 2>&1 | grep -i "To test"
 
 about:
-  home: https://github.com/oushujun/EDTA
-  license: GPL-3.0-only
+  home: "https://github.com/oushujun/EDTA"
+  license: "GPL-3.0-only"
   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
+  summary: "Extensive de-novo TE Annotator."
+  dev_url: "https://github.com/oushujun/EDTA"
+  doc_url: "https://github.com/oushujun/EDTA/wiki"
 
 extra:
   identifiers: