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Build branch main with version v0.1.0 (d33eb37)

Browse Source 
Build pipeline: viash-hub.toolbox.main-4f6nw

Source commit: d33eb37068

Source message: Update readme and package config (#13)

* update readme and package config

* update changelog

* update readme

* update readme

* fix url

* make images relative again
This commit is contained in:
CI
2025-05-06 20:17:17 +00:00
parent 39a745c398
commit 36b9c79457
18 changed files with 1236 additions and 475 deletions
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32
target/executable/bgzip/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "bgzip"
version: "main"
version: "v0.1.0"
argument_groups:
- name: "Inputs"
arguments:
@@ -126,6 +126,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -207,7 +210,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/htslib:1.19--h81da01d_0"
target_registry: "images.viash-hub.com"
target_tag: "main"
target_tag: "v0.1.0"
namespace_separator: "/"
setup:
- type: "docker"
@@ -224,22 +227,35 @@ build_info:
engine: "docker|native"
output: "target/executable/bgzip"
executable: "target/executable/bgzip/bgzip"
viash_version: "0.9.0"
git_commit: "a3cebc0315249e08a4a39d175670f29a800c1c5f"
viash_version: "0.9.4"
git_commit: "d33eb370683ba1f1132ec7d7b6884c8040dc901a"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"
version: "main"
description: "A collection of command-line tools.\n"
version: "v0.1.0"
summary: "A collection of curated command-line tools for general IT tasks, built\
\ with Viash.\n"
description: "`toolbox` provides a versatile suite of IT components, following the\
\ robust Viash (https://viash.io) framework.\nThis package focuses on delivering\
\ reliable, standalone tools that can be easily integrated into larger computational\
\ workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**,\
\ and adherence to **best practices** in component creation. Key features of `toolbox`\
\ components include:\n\n* **Standalone & Nextflow Ready:** Execute components\
\ directly from the command line or seamlessly incorporate them into Nextflow\
\ workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for each component and its parameters.\n * Full exposure of the underlying\
\ tool's arguments for maximum flexibility.\n * Containerized (Docker) to ensure\
\ consistent environments and manage dependencies, leading to enhanced reproducibility.\n\
\ * Unit tested to verify functionality and ensure reliability.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
keywords:
- "toolbox"
- "command-line"

162
target/executable/bgzip/bgzip
View File

@@ -1,8 +1,8 @@
#!/usr/bin/env bash
# bgzip main
# bgzip v0.1.0
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -169,67 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bgzip main"
echo ""
echo "Block compression/decompression utility"
echo ""
echo "Inputs:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " file to be compressed or decompressed"
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " compressed or decompressed output"
echo ""
echo " -I, --index_name"
echo " type: file, output, file must exist"
echo " name of BGZF index file [file.gz.gzi]"
echo ""
echo "Arguments:"
echo " -b, --offset"
echo " type: integer"
echo " decompress at virtual file pointer (0-based uncompressed offset)"
echo ""
echo " -d, --decompress"
echo " type: boolean_true"
echo " decompress the input file"
echo ""
echo " -g, --rebgzip"
echo " type: boolean_true"
echo " use an index file to bgzip a file"
echo ""
echo " -i, --index"
echo " type: boolean_true"
echo " compress and create BGZF index"
echo ""
echo " -l, --compress_level"
echo " type: integer"
echo " min: -1"
echo " max: 9"
echo " compression level to use when compressing; 0 to 9, or -1 for default"
echo " [-1]"
echo ""
echo " -r, --reindex"
echo " type: boolean_true"
echo " (re)index the output file"
echo ""
echo " -s, --size"
echo " type: integer"
echo " min: 0"
echo " decompress INT bytes (uncompressed size)"
echo ""
echo " -t, --test"
echo " type: boolean_true"
echo " test integrity of compressed file"
echo ""
echo " --binary"
echo " type: boolean_true"
echo " Don't align blocks with text lines"
}
# initialise variables
VIASH_MODE='run'
@@ -509,10 +448,10 @@ ENTRYPOINT []
RUN bgzip -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component bgzip"
LABEL org.opencontainers.image.created="2024-09-13T08:50:00Z"
LABEL org.opencontainers.image.created="2025-05-06T20:10:22Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/htslib"
LABEL org.opencontainers.image.revision="a3cebc0315249e08a4a39d175670f29a800c1c5f"
LABEL org.opencontainers.image.version="main"
LABEL org.opencontainers.image.revision="d33eb370683ba1f1132ec7d7b6884c8040dc901a"
LABEL org.opencontainers.image.version="v0.1.0"
VIASHDOCKER
fi
@@ -626,6 +565,93 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bgzip v0.1.0"
echo ""
echo "Block compression/decompression utility"
echo ""
echo "Inputs:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " file to be compressed or decompressed"
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " compressed or decompressed output"
echo ""
echo " -I, --index_name"
echo " type: file, output, file must exist"
echo " name of BGZF index file [file.gz.gzi]"
echo ""
echo "Arguments:"
echo " -b, --offset"
echo " type: integer"
echo " decompress at virtual file pointer (0-based uncompressed offset)"
echo ""
echo " -d, --decompress"
echo " type: boolean_true"
echo " decompress the input file"
echo ""
echo " -g, --rebgzip"
echo " type: boolean_true"
echo " use an index file to bgzip a file"
echo ""
echo " -i, --index"
echo " type: boolean_true"
echo " compress and create BGZF index"
echo ""
echo " -l, --compress_level"
echo " type: integer"
echo " min: -1"
echo " max: 9"
echo " compression level to use when compressing; 0 to 9, or -1 for default"
echo " [-1]"
echo ""
echo " -r, --reindex"
echo " type: boolean_true"
echo " (re)index the output file"
echo ""
echo " -s, --size"
echo " type: integer"
echo " min: 0"
echo " decompress INT bytes (uncompressed size)"
echo ""
echo " -t, --test"
echo " type: boolean_true"
echo " test integrity of compressed file"
echo ""
echo " --binary"
echo " type: boolean_true"
echo " Don't align blocks with text lines"
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''
@@ -648,7 +674,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "bgzip main"
echo "bgzip v0.1.0"
exit
;;
--input)
@@ -884,7 +910,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/bgzip:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/bgzip:v0.1.0'
fi
# print dockerfile

32
target/executable/yq/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "yq"
version: "main"
version: "v0.1.0"
argument_groups:
- name: "Inputs"
arguments:
@@ -149,6 +149,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -234,7 +237,7 @@ engines:
id: "docker"
image: "alpine:latest"
target_registry: "images.viash-hub.com"
target_tag: "main"
target_tag: "v0.1.0"
namespace_separator: "/"
setup:
- type: "apk"
@@ -254,22 +257,35 @@ build_info:
engine: "docker|native"
output: "target/executable/yq"
executable: "target/executable/yq/yq"
viash_version: "0.9.0"
git_commit: "a3cebc0315249e08a4a39d175670f29a800c1c5f"
viash_version: "0.9.4"
git_commit: "d33eb370683ba1f1132ec7d7b6884c8040dc901a"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"
version: "main"
description: "A collection of command-line tools.\n"
version: "v0.1.0"
summary: "A collection of curated command-line tools for general IT tasks, built\
\ with Viash.\n"
description: "`toolbox` provides a versatile suite of IT components, following the\
\ robust Viash (https://viash.io) framework.\nThis package focuses on delivering\
\ reliable, standalone tools that can be easily integrated into larger computational\
\ workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**,\
\ and adherence to **best practices** in component creation. Key features of `toolbox`\
\ components include:\n\n* **Standalone & Nextflow Ready:** Execute components\
\ directly from the command line or seamlessly incorporate them into Nextflow\
\ workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for each component and its parameters.\n * Full exposure of the underlying\
\ tool's arguments for maximum flexibility.\n * Containerized (Docker) to ensure\
\ consistent environments and manage dependencies, leading to enhanced reproducibility.\n\
\ * Unit tested to verify functionality and ensure reliability.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
keywords:
- "toolbox"
- "command-line"

128
target/executable/yq/yq
View File

@@ -1,8 +1,8 @@
#!/usr/bin/env bash
# yq main
# yq v0.1.0
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -169,50 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "yq main"
echo ""
echo "A portable YAML, JSON, XML, CSV, TOML and properties processor"
echo ""
echo "Inputs:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " example: input.yaml"
echo " files to be processed"
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.yaml"
echo " output file"
echo ""
echo "Arguments:"
echo " --eval"
echo " type: string, required parameter"
echo " example: .name = \"foo\""
echo " expression to evaluate"
echo ""
echo " -I, --indent"
echo " type: integer"
echo " sets indent level for output (default 2)"
echo ""
echo " -p, --input_format"
echo " type: string"
echo " choices: [ auto, a, yaml, y, json, j, props, p, csv, c, tsv, t, xml, x,"
echo "base64, uri, toml, shell, s, lua, l ]"
echo " parse format for input. (default \"auto\")"
echo ""
echo " -o, --output_format"
echo " type: string"
echo " choices: [ auto, a, yaml, y, json, j, props, p, csv, c, tsv, t, xml, x,"
echo "base64, uri, toml, shell, s, lua, l ]"
echo " output format type. (default \"auto\")"
echo ""
echo " -P, --pretty_print"
echo " type: boolean_true"
echo " pretty print, shorthand for '... style = \"\"'"
}
# initialise variables
VIASH_MODE='run'
@@ -494,10 +450,10 @@ RUN apk add --no-cache bash yq-go
RUN /usr/bin/yq --version | sed 's/.*version\sv\(.*\)/yq: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component yq"
LABEL org.opencontainers.image.created="2024-09-13T08:49:59Z"
LABEL org.opencontainers.image.created="2025-05-06T20:10:22Z"
LABEL org.opencontainers.image.source="https://github.com/mikefarah/yq"
LABEL org.opencontainers.image.revision="a3cebc0315249e08a4a39d175670f29a800c1c5f"
LABEL org.opencontainers.image.version="main"
LABEL org.opencontainers.image.revision="d33eb370683ba1f1132ec7d7b6884c8040dc901a"
LABEL org.opencontainers.image.version="v0.1.0"
VIASHDOCKER
fi
@@ -611,6 +567,76 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "yq v0.1.0"
echo ""
echo "A portable YAML, JSON, XML, CSV, TOML and properties processor"
echo ""
echo "Inputs:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " example: input.yaml"
echo " files to be processed"
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.yaml"
echo " output file"
echo ""
echo "Arguments:"
echo " --eval"
echo " type: string, required parameter"
echo " example: .name = \"foo\""
echo " expression to evaluate"
echo ""
echo " -I, --indent"
echo " type: integer"
echo " sets indent level for output (default 2)"
echo ""
echo " -p, --input_format"
echo " type: string"
echo " choices: [ auto, a, yaml, y, json, j, props, p, csv, c, tsv, t, xml, x,"
echo "base64, uri, toml, shell, s, lua, l ]"
echo " parse format for input. (default \"auto\")"
echo ""
echo " -o, --output_format"
echo " type: string"
echo " choices: [ auto, a, yaml, y, json, j, props, p, csv, c, tsv, t, xml, x,"
echo "base64, uri, toml, shell, s, lua, l ]"
echo " output format type. (default \"auto\")"
echo ""
echo " -P, --pretty_print"
echo " type: boolean_true"
echo " pretty print, shorthand for '... style = \"\"'"
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''
@@ -633,7 +659,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "yq main"
echo "yq v0.1.0"
exit
;;
--input)
@@ -818,7 +844,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/yq:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/yq:v0.1.0'
fi
# print dockerfile