[ci skip] Merge PR 36787

Merge PR #36787, commits were: 
 * fix quote
 * quiet down curl
 * update patch files for v2
 * Update sra-human-scrubber to 2.0.0
 * Update sra-human-scrubber to 1.1.0

recipes/sra-human-scrubber/build.sh

@@ -1,5 +1,15 @@
 #!/bin/bash
 
+# Setup shared directory
+SHARE_DIR="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}"
+mkdir -p ${SHARE_DIR}/data
+cp -r ./test ${SHARE_DIR}/
+touch ${SHARE_DIR}/data/sra-human-scrubber-placeholder.txt
+
+# Replace with share directory path
+sed -i "s=BIOCONDA_SED_REPLACE=$SHARE_DIR=" init_db.sh
+sed -i "s=BIOCONDA_SED_REPLACE=$SHARE_DIR=" scripts/scrub.sh
+
 # Add scripts
 mkdir -p ${PREFIX}/bin
 chmod 755 bin/*
@@ -8,20 +18,3 @@ chmod 755 scripts/*
 cp scripts/* ${PREFIX}/bin
 chmod 755 init_db.sh
 cp init_db.sh ${PREFIX}/bin
-
-# Setup shared directory
-SHARE_DIR="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}"
-mkdir -p ${SHARE_DIR}/data
-cp -r ./test ${SHARE_DIR}/
-touch ${SHARE_DIR}/data/sra-human-scrubber-placeholder.txt
-
-# Setup the VADR env variables
-mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d
-echo "export SCRUBBER_ROOT=${PREFIX}" > ${PREFIX}/etc/conda/activate.d/sra-human-scrubber.sh
-echo "export SCRUBBER_SHARE=${SHARE_DIR}" >> ${PREFIX}/etc/conda/activate.d/sra-human-scrubber.sh
-chmod a+x ${PREFIX}/etc/conda/activate.d/sra-human-scrubber.sh
-
-# Unset them
-echo "unset SCRUBBER_ROOT" > ${PREFIX}/etc/conda/deactivate.d/sra-human-scrubber.sh
-echo "unset SCRUBBER_SHARE" >> ${PREFIX}/etc/conda/deactivate.d/sra-human-scrubber.sh
-chmod a+x ${PREFIX}/etc/conda/deactivate.d/sra-human-scrubber.sh

recipes/sra-human-scrubber/fix_init_db_path.patch

@@ -1,11 +1,18 @@
 diff --git a/init_db.sh b/init_db.sh
-index 54abf86..435351a 100755
+index de67e29..03a69c5 100755
 --- a/init_db.sh
 +++ b/init_db.sh
-@@ -1,5 +1,5 @@
+@@ -1,7 +1,10 @@
  #!/bin/bash
  set -eu
 
--curl -vf "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter.db" -o ./data/human_filter.db
-+curl -vf "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter.db" -o ${SCRUBBER_SHARE}/data/human_filter.db
++SCRUBBER_SHARE=BIOCONDA_SED_REPLACE
+ VERSION=$(curl "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter/current/version.txt")
+-cd data && curl -vf "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter/${VERSION}.human_filter.db" -o "${VERSION}.human_filter.db"
+-ln -s "${VERSION}".human_filter.db human_filter.db
++cd ${SCRUBBER_SHARE}/data && \
++  curl -f "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter/${VERSION}.human_filter.db" -o "${VERSION}.human_filter.db" &&
++  ln -s -f "${VERSION}".human_filter.db human_filter.db
++
  exit 0
+

recipes/sra-human-scrubber/fix_scrub_path.patch

@@ -1,28 +1,48 @@
 diff --git a/scripts/scrub.sh b/scripts/scrub.sh
-index fc2f35c..1fdfaab 100755
+index f6b310c..6848a94 100755
 --- a/scripts/scrub.sh
 +++ b/scripts/scrub.sh
-@@ -27,17 +27,17 @@ done
- shift $((OPTIND-1))
- fastq="$1"
+@@ -27,7 +27,8 @@ RUNTEST=false
+ THREADS=
  DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )"  >/dev/null 2>&1 && pwd  )"
--ROOT=$(dirname $DIR)
+ ROOT=$(dirname $DIR)
 -DB=$ROOT/data/human_filter.db
-+ROOT=${SCRUBBER_ROOT}
++SCRUBBER_SHARE=BIOCONDA_SED_REPLACE
 +DB=${SCRUBBER_SHARE}/data/human_filter.db
 
--if [ "$1" == "test" ] && [ -e "$ROOT/test/scrubber_test.fastq" ];
-+if [ "$1" == "test" ] && [ -e "${SCRUBBER_SHARE}/test/scrubber_test.fastq" ];
+ #Get input
+ while getopts ":i:o:d:p:hxrt" opts; do
+@@ -65,10 +66,10 @@ if [ "$INFILE" == "test" ];
+ fi
+
+ #TESTING create temp dir and set infile
+-if $RUNTEST && [ -e "$ROOT/test/scrubber_test.fastq" ];
++if $RUNTEST && [ -e "${SCRUBBER_SHARE}/test/scrubber_test.fastq" ];
    then
      TMP_DIR=$(mktemp -d)
 -    cp "$ROOT"/test/* "$TMP_DIR/"
 +    cp "${SCRUBBER_SHARE}"/test/* "$TMP_DIR/"
-     fastq=$TMP_DIR/scrubber_test.fastq
+     INFILE=$TMP_DIR/scrubber_test.fastq
+ fi
+
+@@ -85,17 +86,17 @@ if [ ! -e "${INFILE}" ];
+     INFILE="$TMP_F_DIR/temp.fastq"
  fi
--python "$ROOT/scripts/fastq_to_fasta.py" < "$fastq" > "$fastq.fasta"
--${ROOT}/bin/aligns_to -db "$ROOT/data/human_filter.db" "$fastq.fasta" | "$ROOT/scripts/cut_spots_fastq.py" "$fastq" ${OPTS} > "$fastq.clean"
-+fastq_to_fasta.py < "$fastq" > "$fastq.fasta"
-+aligns_to -db "${DB}" "$fastq.fasta" | cut_spots_fastq.py "$fastq" ${OPTS} > "$fastq.clean"
- if [ "$1" == "test" ];
+ #Use infile or temp fastq and generate fasta
+-"$ROOT/scripts/fastq_to_fasta.py" < "${INFILE}" > "$TMP_F_DIR/temp.fasta"
++fastq_to_fasta.py < "${INFILE}" > "$TMP_F_DIR/temp.fasta"
+ 
+ if [ "$OUTFILE" ] && [ "$OUTFILE" != "-" ];
    then
-     if [ -e "$TMP_DIR/scrubber_test.fastq.clean" ] &&
+-    "${ROOT}"/bin/aligns_to -db "${DB}" $(if [[ "$THREADS" =~ ^[0-9]+$ ]]; then printf "%s" "-num_threads $THREADS"; fi) "$TMP_F_DIR/temp.fasta" | "$ROOT/scripts/cut_spots_fastq.py" "$INFILE" "$REPLACEN" "$SAVEIDSPOTS" > "$OUTFILE"
++    aligns_to -db "${DB}" $(if [[ "$THREADS" =~ ^[0-9]+$ ]]; then printf "%s" "-num_threads $THREADS"; fi) "$TMP_F_DIR/temp.fasta" | cut_spots_fastq.py "$INFILE" "$REPLACEN" "$SAVEIDSPOTS" > "$OUTFILE"
+     if [ "$SAVEIDSPOTS" ] && [ -e "$TMP_F_DIR/temp.fastq.removed_spots" ];
+       then
+         cp "$TMP_F_DIR/temp.fastq.removed_spots" "$OUTFILE.removed_spots"
+     fi
+     else
+-      "${ROOT}"/bin/aligns_to -db "${DB}" $(if [[ "$THREADS" =~ ^[0-9]+$ ]]; then printf "%s" "-num_threads $THREADS"; fi) "$TMP_F_DIR/temp.fasta" | "$ROOT/scripts/cut_spots_fastq.py" "$INFILE" "$REPLACEN"
++      aligns_to -db "${DB}" $(if [[ "$THREADS" =~ ^[0-9]+$ ]]; then printf "%s" "-num_threads $THREADS"; fi) "$TMP_F_DIR/temp.fasta" | cut_spots_fastq.py "$INFILE" "$REPLACEN"
+ fi
+
+ #Check if TESTING was successful

recipes/sra-human-scrubber/meta.yaml

@@ -1,14 +1,14 @@
 
 {% set name = "sra-human-scrubber" %}
-{% set version = "1.0.2021_05_05" %}
+{% set version = "2.0.0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   - url: https://github.com/ncbi/{{ name }}/archive/refs/tags/{{ version|replace("_", "-") }}.tar.gz
-    sha256: ccedb2c253e8db560a08c2f78139c50f84eb2bb5870914a23b7007f920969fe4
+    sha256: c4c9078325b01c7aa8bc0bcdee37f2b102880d66e478d19858eef1f00056d435
     patches:
       - fix_scrub_path.patch
       - fix_init_db_path.patch

recipes/sra-human-scrubber/post-link.sh

@@ -2,6 +2,4 @@
 
 echo "
 Please run 'init_db.sh' to download the database required to run sra-human-scrubber. 
-These files will be downloaded to ${SCRUBBER_SHARE}/data. 
 " >> ${PREFIX}/.messages.txt
-printf '%s\n' "${URLS[@]}" >> "${PREFIX}/.messages.txt" 2>&1