Update Kalamari

recipes/kalamari/build.sh

@@ -1,20 +1,18 @@
 #!/bin/bash
 
-mkdir -p $PREFIX/bin
+mkdir -pv $PREFIX/bin
+mkdir -pv $PREFIX/src
+mkdir -pv $PREFIX/share/${PKG_NAME}-${PKG_VERSION}
 
 # Add in the correct version for the build
 sed -i.bak "s/VERSION=.\+/VERSION=\"${PKG_VERSION}\"/" bin/downloadKalamari.sh
 
-# Copy the executable files to the correct location
-EXES="downloadKalamari.pl downloadKalamari.sh generate_sepia_reference.py  getExactTaxonomy.pl  mobsuiteRepresentativeFasta.pl  validateTaxonomy.pl"
-for i in $EXES; do
-  chmod -v 755 bin/$i
-  cp -vf bin/$i $PREFIX/bin
+for i in bin/*.pl bin/*.sh bin/*.py; do
+  chmod -v 755 $i
+  cp -vf $i $PREFIX/bin/
 done
 
-# Copy the source files to the correct location
-mkdir -p $PREFIX/src
-SRC="chromosomes.tsv plasmids.tsv taxonomy"
-for i in $SRC; do
-  cp -rvf src/$i $PREFIX/src
+for i in src/*.tsv; do 
+  cp -vf $i $PREFIX/src/
 done
+cp -rvf src/taxonomy $PREFIX/src/

recipes/kalamari/meta.yaml

@@ -10,7 +10,7 @@ source:
   sha256: bf465c9212345f7a11da6cfe42da6fc3455d4e517fb8610ae9cfe7e8dfaa2f81
 
 build:
-  number: 0
+  number: 2
   noarch: generic
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x") }}
@@ -20,14 +20,10 @@ requirements:
     - perl
     - perl-module-build
     - entrez-direct
-    - kraken >=1,<2
-    - kraken2
   run:
     - perl
     - perl-module-build
     - entrez-direct
-    - kraken >=1,<2
-    - kraken2
 
 test:
   commands:

recipes/kalamari/post-link.sh

@@ -8,10 +8,13 @@ This will load the files into:
 
 * $DB_PREFIX/kalamari - the genomic files
 
-Suggested directories if building databases:
+The following databases are available:
+* buildTaxonomy.sh  - builds a modified taxonomy directory at $DB_PREFIX/taxonomy
+* filterTaxonomy.sh - filters the taxonomy directory into just taxa that are used in Kalamari into $DB_PREFIX/taxonomy/filtered (requires taxonkit)
 
-* $DB_PREFIX/kraken1.kalamari - the Kraken1 database
-* $DB_PREFIX/kraken2.kalamari - the Kraken2 database
+The following depend on a built taxonomy from buildTaxonomy.sh
+* buildKraken1.sh - creates a Kraken1 database at $DB_PREFIX/kraken.kalamari (requires filterTaxonomy.sh, Kraken1)
+* buildKraken2.sh - creates a Kraken2 database at $DB_PREFIX/kraken2.kalamari (requires filterTaxonomy.sh, Kraken2)
 
 For more refined options, please start with
   downloadKalamari.pl --help