Updated kraken2-db

updated alphafold db

easyconfigs/a/alphafold-db/alphafold-db-20230405.eb

@@ -15,7 +15,7 @@ dependencies = []
 
 sanity_check_paths = {
         'files': [],
-        'dirs': ['bfd','mgnify','params','pdb70','pdb_mmcif','uniclust30','uniref90'],
+        'dirs': ['bfd','mgnify','params','pdb70','pdb_mmcif','uniref90'],
 }
 
 modextrapaths = {

easyconfigs/k/kraken2-db/kraken2-db-20220327.eb

@@ -3,8 +3,8 @@ easyblock = 'Bundle'
 name = 'kraken2-db'
 version = '20220327'
 
-homepage = 'https://ccb.jhu.edu/software/kraken/'
-description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. """
+homepage = 'https://benlangmead.github.io/aws-indexes/k2'
+description = """Kraken 2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. """
 
 toolchain = SYSTEM
 

easyconfigs/k/kraken2-db/kraken2-db-20230314.eb

@@ -0,0 +1,29 @@
+easyblock = 'Bundle'
+
+name = 'kraken2-db'
+version = '20230314'
+
+homepage = 'https://benlangmead.github.io/aws-indexes/k2'
+description = """Kraken 2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. """
+
+toolchain = SYSTEM
+
+source_urls = ['']
+sources = []
+
+dependencies = []
+
+sanity_check_paths = {
+        'files': [],
+        'dirs': ['k2_standard','k2_pluspfp','k2_pluspf','k2_minusb','k2_viral','k2_eupathdb48'],
+}
+
+modextrapaths = {
+	'BIODB':''
+}
+
+keeppreviousinstall = True
+moduleclass = 'data'
+
+modloadmsg = "%(name)s/%(version)s database is located at %(installdir)s\n"
+

easyconfigs/k/kraken2-db/kraken2-db_download.sh

@@ -0,0 +1,58 @@
+#!/bin/bash
+# ----------------SLURM Parameters----------------
+#SBATCH -p admin
+#SBATCH -n 1
+#SBATCH --mem=20g
+#SBATCH -N 1
+#SBATCH --mail-user=datamover@igb.illinois.edu
+#SBATCH --mail-type=ALL
+#SBATCH -J DATABASE_download
+#SBATCH -D /home/a-m/datamover/jobs
+#SBATCH -o %x-%j.out
+# ----------------Load Modules--------------------
+# ----------------Commands------------------------
+#
+# Replace DATABASE with name of database you are downloading
+# Replace WEBSITE with remote location of database
+#
+
+DATABASE="kraken2-db"
+
+if [ -z "$1" ];
+then
+	echo "Please specify ${DATABASE} version number";
+	exit 1;
+fi
+
+VERSION=$1
+MIRROR_DIR=/private_stores/mirror/${DATABASE}/${VERSION}
+
+echo "`date "+%Y-%m-%d %k:%M:%S"` Downloading Files"
+mkdir -p ${MIRROR_DIR}
+mkdir -p ${MIRROR_DIR}/k2_viral
+wget -P $MIRROR_DIR/k2_viral https://genome-idx.s3.amazonaws.com/kraken/k2_viral_${VERSION}.tar.gz
+mkdir -p ${MIRROR_DIR}/k2_minusb
+wget -P $MIRROR_DIR/k2_minusb https://genome-idx.s3.amazonaws.com/kraken/k2_minusb_${VERSION}.tar.gz
+mkdir -p ${MIRROR_DIR}/k2_standard
+wget -P $MIRROR_DIR/k2_standard https://genome-idx.s3.amazonaws.com/kraken/k2_standard_${VERSION}.tar.gz
+wget -P $MIRROR_DIR https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_${VERSION}.tar.gz
+mkdir -p ${MIRROR_DIR}/k2_standard_16gb
+wget -P $MIRROR_DIR/k2_standard_16gb  https://genome-idx.s3.amazonaws.com/kraken/k2_standard_16gb_${VERSION}.tar.gz
+mkdir -p ${MIRROR_DIR}/k2_pluspf
+wget -P $MIRROR_DIR/k2_pluspf  https://genome-idx.s3.amazonaws.com/kraken/k2_pluspf_${VERSION}.tar.gz
+mkdir -p ${MIRROR_DIR}/k2_pluspf_08gb
+wget -P $MIRROR_DIR/k2_pluspf_08gb https://genome-idx.s3.amazonaws.com/kraken/k2_pluspf_08gb_${VERSION}.tar.gz
+mkdir -p ${MIRROR_DIR}/k2_pluspf_16gb
+wget -P $MIRROR_DIR/k2_pluspf_16gb https://genome-idx.s3.amazonaws.com/kraken/k2_pluspf_16gb_${VERSION}.tar.gz
+mkdir -p ${MIRROR_DIR}/k2_pluspfp
+wget -P $MIRROR_DIR/k2_pluspfp https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_${VERSION}.tar.gz
+mkdir -p ${MIRROR_DIR}/k2_pluspfp_08gb
+wget -P $MIRROR_DIR/k2_pluspfp_08gb https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_08gb_${VERSION}.tar.gz
+mkdir -p ${MIRROR_DIR}/k2_pluspfp_16gb
+wget -P $MIRROR_DIR}/k2_pluspfp_16gb https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_16gb_${VERSION}.tar.gz
+mkdir -p ${MIRROR_DIR}/k2_eupathdb48
+wget -P $MIRROR_DIR/k2_eupathdb48 https://genome-idx.s3.amazonaws.com/kraken/k2_eupathdb48_20201113.tar.gz
+
+
+
+

easyconfigs/k/kraken2-db/kraken2-db_extract.db

@@ -0,0 +1,61 @@
+#!/bin/bash
+# ----------------SLURM Parameters----------------
+#SBATCH -p admin
+#SBATCH -n 4
+#SBATCH --mem=20g
+#SBATCH -N 1
+#SBATCH --mail-user=datamover@igb.illinois.edu
+#SBATCH --mail-type=ALL
+#SBATCH -J DATABASE_extract
+#SBATCH -D /home/a-m/datamover/jobs
+#SBATCH -o %x-%j.out
+# ----------------Load Modules--------------------
+module load pigz/2.4-IGB-gcc-8.2.0
+# ----------------Commands------------------------
+#
+# Replace DATABASE with name of database you are downloading
+# Replace WEBSITE with remote location of database#
+#
+
+DATABASE="kraken2-db"
+
+if [ -z "$1" ];
+then
+	echo "Please specify ${DATABASE} version number";
+	exit 1;
+fi
+
+VERSION=$1
+MIRROR_DIR=/private_stores/mirror/${DATABASE}/${VERSION}
+
+
+echo "`date "+%Y-%m-%d %k:%M:%S"` Extracting Files"
+
+echo "`date "+%Y-%m-%d %k:%M:%S"` Extracting Files"
+for f in $(find ${MIRROR_DIR} -name '*.tar.gz');
+do
+	pigz -p $SLURM_NTASKS -dc $f | tar xf -
+        if [ $? -ne 0 ]; then
+                echo "`date "+%Y-%m-%d %k:%M:%S"` Error extracting file: $f"
+                exit 1
+        else
+                echo "`date "+%Y-%m-%d %k:%M:%S"` Done extracting file: $f"
+        fi
+
+done
+
+echo "`date "+%Y-%m-%d %k:%M:%S"` Extracting Files Complete"
+
+if [ $? -ne 0 ]
+then
+	echo "`date "+%Y-%m-%d %k:%M:%S"` Extracting files Failed"
+	exit $?
+else
+	echo "`date "+%Y-%m-%d %k:%M:%S"` Extracting Files Complete"
+fi
+
+echo "`date "+%Y-%m-%d %k:%M:%S"` Fix Permissions Start"
+find ${MIRROR_DIR} -type d -exec chmod 775 {} \;
+find ${MIRROR_DIR} -type f -exec chmod 664 {} \;
+echo "`date "+%Y-%m-%d %k:%M:%S"` Fix Permissions Completed"
+