Mercurial > repos > rhpvorderman > shm_csr
changeset 5:495a521cf9f2 draft
"planemo upload commit 40d62ec3d2fea3c3bac605c976941e1f3b7e2cd4"
| author | rhpvorderman |
|---|---|
| date | Tue, 16 Nov 2021 11:16:06 +0000 |
| parents | c8f02bce10d0 |
| children | ea9d5fc4c001 |
| files | build_container.sh conda_environment.yml container_hash.tsv converttoutf8.py create_container_hash.py involucro shm_clonality.htm shm_csr.htm shm_csr.xml shm_downloads.htm shm_first.htm shm_frequency.htm shm_overview.htm shm_selection.htm shm_transition.htm tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc tests/test_shm_csr.py utf8test.py |
| diffstat | 18 files changed, 66 insertions(+), 17 deletions(-) [+] |
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--- /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 +
--- 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
--- /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
--- /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() + + + +
--- /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()
--- 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 @@ <html> <head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <meta name=Generator content="Microsoft Word 14 (filtered)"> <style> <!--
--- a/shm_csr.htm Mon Nov 15 14:04:10 2021 +0000 +++ b/shm_csr.htm Tue Nov 16 11:16:06 2021 +0000 @@ -1,7 +1,7 @@ <html> <head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <meta name=Generator content="Microsoft Word 14 (filtered)"> <style> <!--
--- a/shm_csr.xml Mon Nov 15 14:04:10 2021 +0000 +++ b/shm_csr.xml Tue Nov 16 11:16:06 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="shm_csr" name="SHM & CSR pipeline" version="1.3.2.1"> +<tool id="shm_csr" name="SHM & CSR pipeline" version="1.3.2.2"> <description></description> <requirements> <requirement type="package" version="3.7.1">python</requirement> @@ -18,6 +18,8 @@ <requirement type="package" version="5.39">file</requirement> <requirement type="package" version="4.6.0">findutils</requirement> <requirement type="package" version="1.07.1">bc</requirement> + <requirement type="package" version="0.83">font-ttf-ubuntu</requirement> + <container type="docker">quay.io/rhpvorderman/mulled-v2-f7d31c9d7424063a492fc0e5ecbf89bc757c0107:2b50bdd4d8c1fefc6ec24b0753fad0dcecec843b-0</container> </requirements> <command interpreter="bash"> #if str ( $filter_unique.filter_unique_select ) == "remove":
--- a/shm_downloads.htm Mon Nov 15 14:04:10 2021 +0000 +++ b/shm_downloads.htm Tue Nov 16 11:16:06 2021 +0000 @@ -1,7 +1,7 @@ <html> <head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <meta name=Generator content="Microsoft Word 14 (filtered)"> <style> <!--
--- a/shm_first.htm Mon Nov 15 14:04:10 2021 +0000 +++ b/shm_first.htm Tue Nov 16 11:16:06 2021 +0000 @@ -1,7 +1,7 @@ <html> <head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <meta name=Generator content="Microsoft Word 14 (filtered)"> <style> <!--
--- a/shm_frequency.htm Mon Nov 15 14:04:10 2021 +0000 +++ b/shm_frequency.htm Tue Nov 16 11:16:06 2021 +0000 @@ -1,7 +1,7 @@ <html> <head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <meta name=Generator content="Microsoft Word 14 (filtered)"> <style> <!--
--- a/shm_overview.htm Mon Nov 15 14:04:10 2021 +0000 +++ b/shm_overview.htm Tue Nov 16 11:16:06 2021 +0000 @@ -1,7 +1,7 @@ <html> <head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <meta name=Generator content="Microsoft Word 14 (filtered)"> <style> <!--
--- a/shm_selection.htm Mon Nov 15 14:04:10 2021 +0000 +++ b/shm_selection.htm Tue Nov 16 11:16:06 2021 +0000 @@ -1,7 +1,7 @@ <html> <head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <meta name=Generator content="Microsoft Word 14 (filtered)"> <style> <!--
--- a/shm_transition.htm Mon Nov 15 14:04:10 2021 +0000 +++ b/shm_transition.htm Tue Nov 16 11:16:06 2021 +0000 @@ -1,7 +1,7 @@ <html> <head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta http-equiv=Content-Type content="text/html; charset=UTF-8"> <meta name=Generator content="Microsoft Word 14 (filtered)"> <style> <!--
--- a/tests/test_shm_csr.py Mon Nov 15 14:04:10 2021 +0000 +++ b/tests/test_shm_csr.py Tue Nov 16 11:16:06 2021 +0000 @@ -36,6 +36,7 @@ @pytest.fixture(scope="module") def shm_csr_result(): + docker_container = "quay.io/rhpvorderman/mulled-v2-f7d31c9d7424063a492fc0e5ecbf89bc757c0107:2b50bdd4d8c1fefc6ec24b0753fad0dcecec843b-0" temp_dir = Path(tempfile.mkdtemp()) tool_dir = temp_dir / "shm_csr" shutil.copytree(GIT_ROOT, tool_dir) @@ -84,9 +85,13 @@ empty_region_filter, fast ] + docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}", + "-v", f"{input}:{input}", + "-w", str(working_dir), + docker_container] + cmd with open(temp_dir / "stderr", "wt") as stderr_file: with open(temp_dir / "stdout", "wt") as stdout_file: - subprocess.run(cmd, cwd=working_dir, stdout=stdout_file, + subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file, stderr=stderr_file, check=True) yield Path(out_files_path) #shutil.rmtree(temp_dir)