tservice-plugins
/
quartet-rnaseq-report
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Fix dependencies.

tags/v0.1.2
YJC пре 3 година
родитељ
d5bb973165
комит
c99aa2cd7a
6 измењених фајлова са 304 додато и 235 уклоњено
Један поглед
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  1. +1
    -1
      project.clj
  2. BIN
      resources/quartet-rnaseq-report.tar.gz
  3. +125
    -0
      resources/quartet-rnaseq-report/bin/exp2qcdt.sh
  4. +177
    -233
      resources/renv.lock
  5. +1
    -0
      resources/renv/settings.dcf
  6. +0
    -1
      resources/tservice-plugin.yaml

+ 1
- 1
project.clj Прегледај датотеку

(defproject tservice-plugins/quartet-rnaseq-report "v0.1.1"
(defproject tservice-plugins/quartet-rnaseq-report "v0.1.2"
:description "QC Report for Quartet RNA-Seq." :description "QC Report for Quartet RNA-Seq."
:url "https://github.com/tservice-plugins/quartet-rnaseq-report" :url "https://github.com/tservice-plugins/quartet-rnaseq-report"
:license {:name "Eclipse Public License" :license {:name "Eclipse Public License"

BIN
resources/quartet-rnaseq-report.tar.gz Прегледај датотеку


+ 125
- 0
resources/quartet-rnaseq-report/bin/exp2qcdt.sh Прегледај датотеку

#!/usr/bin/env bash

# A wrapper for exp2qcdt r package
#
# Author: Jingcheng Yang
# Email: yjcyxky@163.com
#
# License: MIT

# Exit on error. Append "|| true" if you expect an error.
# set -o errexit
# Exit on error inside any functions or subshells.
# set -o errtrace
# Do not allow use of undefined vars. Use ${VAR:-} to use an undefined VAR
set -o nounset
# Catch the error in case mysqldump fails (but gzip succeeds) in `mysqldump |gzip`
set -o pipefail
# Turn on traces, useful while debugging but commented out by default
# set -o xtrace

show_help() {
cat <<EOF
usage: $(echo $0) [-e <FPKM_FILE>] [-c <COUNT_FILE>][-m <META_FILE>] [-o <RESULT_DIR>]
-e FPKM_FILE Fpkm table file.
-c COUNT_FILE Count table file
-m META_FILE Metadata file.
-o RESULT_DIR A directory for result files.
EOF
}

while getopts ":he:c:m:o:" arg; do
case "$arg" in
"e")
FPKM_FILE="$OPTARG"
;;
"c")
COUNT_FILE="$OPTARG"
;;
"m")
META_FILE="$OPTARG"
;;
"o")
RESULT_DIR="$OPTARG"
;;
"?")
echo "Unkown option: $OPTARG"
exit 1
;;
":")
echo "No argument value for option $OPTARG"
;;
h)
show_help
exit 0
;;
*)
echo "Unknown error while processing options"
show_help
exit 1
;;
esac
done

if [ -z "$FPKM_FILE" ]; then
echo "-e argument is not specified."
exit 1
elif [ ! -f "$FPKM_FILE" ]; then
echo "$FPKM_FILE is not a valid file."
exit 1
else
FPKM_FILE=$(realpath $FPKM_FILE)
fi

if [ -z "$COUNT_FILE" ]; then
echo "-c argument is not specified."
exit 1
elif [ ! -f "$COUNT_FILE" ]; then
echo "$COUNT_FILE is not a valid file."
exit 1
else
COUNT_FILE=$(realpath $COUNT_FILE)
fi

if [ -z "$META_FILE" ]; then
echo "-m argument is not specified."
exit 1
elif [ ! -f "$META_FILE" ]; then
echo "$META_FILE is not a valid file."
exit 1
else
META_FILE=$(realpath $META_FILE)
fi

if [ -z "$RESULT_DIR" ]; then
echo "-o argument is not specified."
exit 1
elif [ ! -d "$RESULT_DIR" ]; then
echo "$RESULT_DIR is not a valid directory."
exit 1
else
RESULT_DIR=$(realpath $RESULT_DIR)
fi

TEMP=$(mktemp)

echo "Run script: $TEMP"
cat <<EOF >"$TEMP"
#!/usr/bin/env Rscript

run <- function() {
# Print traceback message
on.exit(traceback())
library(exp2qcdt)
print("Running...")
exp2qcdt("$FPKM_FILE", "$COUNT_FILE", "$META_FILE", "$RESULT_DIR")
}

run()
EOF

printf "\n---------------------\n"
cat "$TEMP"
echo "---------------------"

Rscript $TEMP

+ 177
- 233
resources/renv.lock Прегледај датотеку

"Version": "3.10" "Version": "3.10"
}, },
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},
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"Package": "BiocManager", "Package": "BiocManager",
"Version": "1.30.12",
"Version": "1.30.16",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Hash": "462dbb15753eb52fb62e28507f382d2d"
"Hash": "2fdca0877debdd4668190832cdee4c31"
}, },
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"Package": "BiocVersion", "Package": "BiocVersion",
"Source": "Bioconductor", "Source": "Bioconductor",
"Hash": "b69e4e634db423b8e6c58103d579ec95" "Hash": "b69e4e634db423b8e6c58103d579ec95"
}, },
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},
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}, },
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} }
} }
} }

+ 1
- 0
resources/renv/settings.dcf Прегледај датотеку

external.libraries: external.libraries:
ignored.packages: ignored.packages:
package.dependency.fields: Imports, Depends, LinkingTo package.dependency.fields: Imports, Depends, LinkingTo
r.version:
snapshot.type: all snapshot.type: all
use.cache: TRUE use.cache: TRUE
vcs.ignore.library: TRUE vcs.ignore.library: TRUE

+ 0
- 1
resources/tservice-plugin.yaml Прегледај датотеку

# Unpack environment file to the directory, repository/envs/quartet-rnaseq-report # Unpack environment file to the directory, repository/envs/quartet-rnaseq-report
- step: unpack-env - step: unpack-env
envname: quartet-rnaseq-report envname: quartet-rnaseq-report
postunpack: clone-env /opt/local/quartet-rnaseq-report {{ ENV_DEST_DIR }}
- step: load-namespace - step: load-namespace
namespace: tservice.plugins.quartet-rnaseq-report namespace: tservice.plugins.quartet-rnaseq-report
- step: register-plugin - step: register-plugin

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