# HG changeset patch # User rhpvorderman # Date 1637061366 0 # Node ID 495a521cf9f2608976b630c3bb9cd23586b57334 # Parent c8f02bce10d02e531b82518ab8a80ac0e9209e0f "planemo upload commit 40d62ec3d2fea3c3bac605c976941e1f3b7e2cd4" diff -r c8f02bce10d0 -r 495a521cf9f2 build_container.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build_container.sh Tue Nov 16 11:16:06 2021 +0000 @@ -0,0 +1,8 @@ +#!/usr/bin/env bash + +set -e +DEFAULT_BASE_IMAGE="$1" + +python3 create_container_hash.py $DEFAULT_BASE_IMAGE +mulled-build-files --namespace rhpvorderman build-and-test ./container_hash.tsv --verbose + diff -r c8f02bce10d0 -r 495a521cf9f2 conda_environment.yml --- a/conda_environment.yml Mon Nov 15 14:04:10 2021 +0000 +++ b/conda_environment.yml Tue Nov 16 11:16:06 2021 +0000 @@ -19,6 +19,7 @@ - file=5.39 - bc=1.07.1 - findutils=4.6.0 + - font-ttf-ubuntu=0.83 # Test dependencies below - pytest=6.2.5 # Add planemo so tool can be uploaded diff -r c8f02bce10d0 -r 495a521cf9f2 container_hash.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/container_hash.tsv Tue Nov 16 11:16:06 2021 +0000 @@ -0,0 +1,2 @@ +#targets base_image image_build +python=3.7.1,changeo=0.4.4,biopython=1.72,xlrd=1.2.0,r-ggplot2=3.0.0,r-reshape2=1.4.3,r-scales=0.5.0,r-seqinr=3.4_5,r-data.table=1.11.4,unzip=6.0,bash=4.4.18,tar=1.34,file=5.39,findutils=4.6.0,bc=1.07.1,font-ttf-ubuntu=0.83 bgruening/busybox-bash:0.1 0 diff -r c8f02bce10d0 -r 495a521cf9f2 converttoutf8.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/converttoutf8.py Tue Nov 16 11:16:06 2021 +0000 @@ -0,0 +1,9 @@ +#!/usr/bin/env python3 +import sys + +with open(sys.argv[1], "rt", encoding="utf8") as input_h: + input_h.read() + + + + diff -r c8f02bce10d0 -r 495a521cf9f2 create_container_hash.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_container_hash.py Tue Nov 16 11:16:06 2021 +0000 @@ -0,0 +1,29 @@ +#!/usr/bin/env python3 + +import sys + +from xml.etree import ElementTree +from xml.etree.ElementTree import Element + +DEFAULT_BASE_IMAGE = "bgruening/busybox-bash:0.1" +def main(): + try: + base_image = sys.argv[1] + except IndexError: + base_image = DEFAULT_BASE_IMAGE + tool = ElementTree.parse("shm_csr.xml").getroot() + requirements: Element = tool.find("requirements") + packages = [] + for req in requirements.findall("requirement"): + if req.get("type") == "package": + name = req.text + version = req.get("version") + package_string = f"{name}={version}" + packages.append(package_string) + with open("container_hash.tsv", mode="wt") as container_hash_file: + container_hash_file.write("#targets\tbase_image\timage_build\n") + container_hash_file.write(",".join(packages) + f"\t{base_image}\t0\n") + + +if __name__ == "__main__": + main() diff -r c8f02bce10d0 -r 495a521cf9f2 involucro Binary file involucro has changed diff -r c8f02bce10d0 -r 495a521cf9f2 shm_clonality.htm --- a/shm_clonality.htm Mon Nov 15 14:04:10 2021 +0000 +++ b/shm_clonality.htm Tue Nov 16 11:16:06 2021 +0000 @@ -1,7 +1,7 @@ - +