Update Earl Grey meta.yml

recipes/earlgrey/build.sh

@@ -17,10 +17,11 @@ cp -r * ${PACKAGE_HOME}/
 
 
 # Install SA-SSR (has to be done here because SA-SSR is an ancient repository without releases)
-git clone https://github.com/ridgelab/SA-SSR
+git clone --depth 1 https://github.com/ridgelab/SA-SSR
 cd SA-SSR
 make
 cp bin/sa-ssr ${PREFIX}/bin/
+cd ../ && rm -rf SA-SSR/
 
 
 # Fixes to earlGrey executable
@@ -55,10 +56,11 @@ chmod +x ${SCRIPT_DIR}/* > /dev/null 2>&1
 chmod +x ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7/ltr_finder
 chmod a+w ${SCRIPT_DIR}/repeatCraft/example
 
-
 # Extract tRNAdb
-tar -zxf ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7/tRNAdb.tar.gz --directory ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7
+tar -zxf ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7/tRNAdb.tar.gz --directory ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7 && rm -r ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7/tRNAdb.tar.gz
 
+# test for conda
+df -h
 
 # Set PERL5LIB upon activate/deactivate
 for CHANGE in "activate" "deactivate";

recipes/earlgrey/meta.yaml

@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('earlgrey', max_pin='x') }}
 
@@ -20,7 +20,7 @@ requirements:
     - make
     - {{ compiler('cxx') }}
   run:
-    - python =3.8
+    - python =3.9
     - hmmer
     - trf
     - cd-hit
@@ -46,10 +46,16 @@ requirements:
     - r-optparse
     - r-tidyverse
     - r-plyr
+    - r-viridis
+    - r-cowplot
+    - r-ggtext
     - bedtools
+    - emboss
+    - pybedtools
 
 test:
   commands:
+    - df -h
     - earlGrey -h
 
 about:
@@ -61,8 +67,8 @@ about:
     Earl Grey is a full-automated transposable element (TE) annotation pipeline,
     leveraging the most widely-used tools and combining these with a consensus
     elongation process (BEAT) to better define de novo consensus sequences when
-    annotating new genome assemblies. 
+    annotating new genome assemblies.
 
 extra:
   identifiers:
-    - doi:10.1101/2022.06.30.498289
+    - doi:10.1093/molbev/msae068