Mercurial > repos > fubar > toolfactory_gtn
changeset 5:e2c8c2fa192d draft
Uploaded
| author | fubar |
|---|---|
| date | Tue, 27 Apr 2021 23:33:49 +0000 |
| parents | 2a46da701dde |
| children | efefe43f23c8 |
| files | toolfactory/.github/workflows/commit.yml toolfactory/.gitignore toolfactory/.shed.yml toolfactory/README.md toolfactory/ToolFactory.py toolfactory/ToolFactory.xml toolfactory/ToolFactory_tester.py toolfactory/images/TFasIDE.png toolfactory/images/dynamicScriptTool.png toolfactory/images/hello_toolfactory_form.png toolfactory/images/lintplanemo-2021-01-08_18.02.45.mkv toolfactory/install_tf_demos.py toolfactory/maketf.sh toolfactory/test-data/test1_log.txt toolfactory/tfout/.shed.yml toolfactory/tfout/plotter.xml |
| diffstat | 16 files changed, 33 insertions(+), 715 deletions(-) [+] |
line wrap: on
line diff
--- a/toolfactory/.github/workflows/commit.yml Mon Apr 26 05:25:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ -name: Galaxy Tool Linting and Tests for PR -# run planemo on a git repository containing a single tool -# as a github action. -# ross lazarus august 2020 -on: [pull_request,push] -env: - GALAXY_REPO: https://github.com/galaxyproject/galaxy - GALAXY_RELEASE: release_20.05 -jobs: - setup: - name: setup environment and python - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.7] - steps: - - name: Print github context properties - run: | - echo 'event: ${{ github.event_name }}' - echo 'sha: ${{ github.sha }}' - echo 'ref: ${{ github.ref }}' - echo 'head_ref: ${{ github.head_ref }}' - echo 'base_ref: ${{ github.base_ref }}' - echo 'event.before: ${{ github.event.before }}' - echo 'event.after: ${{ github.event.after }}' - - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - uses: actions/checkout@v2 - with: - # planemo does not seem to want to install the requirement galaxyxml - # into the venv it manages at tool testing so do it the old skool way - repository: 'galaxyproject/galaxy' - path: 'galaxy' - - name: make venv ready for this galaxy and planemo - run: | - python3 -m venv $GITHUB_WORKSPACE/galaxy/.venv - . $GITHUB_WORKSPACE/galaxy/.venv/bin/activate - pip install --upgrade pip - pip install wheel - pip install -r $GITHUB_WORKSPACE/galaxy/requirements.txt - - name: Upgrade pip - run: pip install --upgrade pip - # Install the `wheel` package so that when installing other packages which - # are not available as wheels, pip will build a wheel for them, which can be cached. - - name: Install wheel - run: pip install wheel - - name: Install Planemo and flake8 - run: pip install planemo flake8 flake8-import-order - # galaxyxml temporarily removed until PR accepted - - uses: actions/checkout@v2 - with: - fetch-depth: 1 - - name: flake8 *.py - run: flake8 --ignore=E501,E203,W503,C901 - - name: Planemo lint - run: planemo lint . - - name: Planemo test tool - run: planemo test --galaxy_root $GITHUB_WORKSPACE/galaxy --test_output tool_test_output.html --skip_venv --test_output_json tool_test_output.json --galaxy_python_version ${{ matrix.python-version }} . - - name: Copy artifacts into place - run: | - mkdir upload - mv tool_test_output.json tool_test_output.html upload/ - - uses: actions/upload-artifact@v2.0.1 - with: - name: 'All tool test results' - path: upload
--- a/toolfactory/.gitignore Mon Apr 26 05:25:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -pip-wheel-metadata/ -share/python-wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py,cover -.hypothesis/ -.pytest_cache/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -db.sqlite3 -db.sqlite3-journal - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv -.python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -#Pipfile.lock - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow -__pypackages__/ - -# Celery stuff -celerybeat-schedule -celerybeat.pid - -# SageMath parsed files -*.sage.py - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/
--- a/toolfactory/.shed.yml Mon Apr 26 05:25:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -name: toolfactory -owner: fubar -description: ToolFactory - tool to make Galaxy tools ready for the toolshed -homepage_url: https://github.com/fubar2/toolfactory -long_description: | - ToolFactory - turn executable packages and R/python/perl/bash scripts into ordinary Galaxy tools - - Creating re-usable tools from scripts: The Galaxy Tool Factory Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team - Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 -remote_repository_url: https://github.com/fubar2/toolfactory -type: tool_dependency_definition -categories: -- Tool Generators
--- a/toolfactory/README.md Mon Apr 26 05:25:26 2021 +0000 +++ b/toolfactory/README.md Tue Apr 27 23:33:49 2021 +0000 @@ -1,7 +1,9 @@ -## Breaking news! Completely refactored +## Breaking news! Docker container at https://github.com/fubar2/toolfactory-galaxy-docker recommended as at December 2020 ### New demonstration of planemo tool_factory command  +## This is the original ToolFactory suitable for non-docker situations. Please use the docker container if you can because it's integrated with a Toolshed... + # WARNING Install this tool to a throw-away private Galaxy or Docker container ONLY!
--- a/toolfactory/ToolFactory.py Mon Apr 26 05:25:26 2021 +0000 +++ b/toolfactory/ToolFactory.py Tue Apr 27 23:33:49 2021 +0000 @@ -70,146 +70,41 @@ citation_tuples.append(("bibtex", citation[len("bibtex") :].strip())) return citation_tuples -class ToolTester(): - # requires highly insecure docker settings - like write to tool_conf.xml and to tools ! - # if in a container possibly not so courageous. - # Fine on your own laptop but security red flag for most production instances - # uncompress passed tar, run planemo and rebuild a new tarball with tests - - def __init__(self, report_dir, in_tool_archive, new_tool_archive, include_tests, galaxy_root): - self.new_tool_archive = new_tool_archive - self.include_tests = include_tests - self.galaxy_root = galaxy_root - self.repdir = report_dir - assert in_tool_archive and tarfile.is_tarfile(in_tool_archive) - # this is not going to go well with arbitrary names. TODO introspect tool xml! - tff = tarfile.open(in_tool_archive, "r:*") - flist = tff.getnames() - ourdir = os.path.commonpath(flist) # eg pyrevpos - self.tool_name = ourdir - ourxmls = [x for x in flist if x.lower().endswith('.xml') and os.path.split(x)[0] == ourdir] - # planemo_test/planemo_test.xml - assert len(ourxmls) > 0 - self.ourxmls = ourxmls # [os.path.join(tool_path,x) for x in ourxmls] - res = tff.extractall() - tff.close() - self.update_tests(ourdir) - self.tooloutdir = ourdir - self.testdir = os.path.join(self.tooloutdir, "test-data") - if not os.path.exists(self.tooloutdir): - os.mkdir(self.tooloutdir) - if not os.path.exists(self.testdir): - os.mkdir(self.testdir) - if not os.path.exists(self.repdir): - os.mkdir(self.repdir) - if not os.path.exists(self.tooloutdir): - os.mkdir(self.tooloutdir) - if not os.path.exists(self.testdir): - os.mkdir(self.testdir) - if not os.path.exists(self.repdir): - os.mkdir(self.repdir) - self.moveRunOutputs() - self.makeToolTar() - - def call_planemo(self,xmlpath,ourdir): - penv = os.environ - penv['HOME'] = os.path.join(self.galaxy_root,'planemo') - #penv["GALAXY_VIRTUAL_ENV"] = os.path.join(penv['HOME'],'.planemo','gx_venv_3.9') - penv["PIP_CACHE_DIR"] = os.path.join(self.galaxy_root,'pipcache') - toolfile = os.path.split(xmlpath)[1] - tool_name = self.tool_name - tool_test_output = os.path.join(self.repdir, f"{tool_name}_planemo_test_report.html") - cll = ["planemo", - "test", - #"--job_config_file", - # os.path.join(self.galaxy_root,"config","job_conf.xml"), - #"--galaxy_python_version", - #"3.9", - "--test_output", - os.path.abspath(tool_test_output), - "--galaxy_root", - self.galaxy_root, - "--update_test_data", - os.path.abspath(xmlpath), - ] - print("Call planemo cl =", cll) - p = subprocess.run( - cll, - capture_output=True, - encoding='utf8', - env = penv, - shell=False, - ) - return p - - def makeToolTar(self): - """move outputs into test-data and prepare the tarball""" - excludeme = "_planemo_test_report.html" - - def exclude_function(tarinfo): - filename = tarinfo.name - return None if filename.endswith(excludeme) else tarinfo - - newtar = 'new_%s_toolshed.gz' % self.tool_name - ttf = tarfile.open(newtar, "w:gz") - ttf.add(name=self.tooloutdir, - arcname=self.tool_name, - filter=exclude_function) - ttf.close() - shutil.copyfile(newtar, self.new_tool_archive) - - def move_One(self,scandir): - with os.scandir('.') as outs: - for entry in outs: - newname = entry.name - if not entry.is_file() or entry.name.endswith('_sample'): - continue - if not (entry.name.endswith('.html') or entry.name.endswith('.gz') or entry.name.endswith(".tgz")): - fname, ext = os.path.splitext(entry.name) - if len(ext) > 1: - newname = f"{fname}_{ext[1:]}.txt" - else: - newname = f"{fname}.txt" - dest = os.path.join(self.repdir, newname) - src = entry.name - shutil.copyfile(src, dest) - - def moveRunOutputs(self): - """need to move planemo or run outputs into toolfactory collection""" - self.move_One(self.tooloutdir) - self.move_One('.') - if self.include_tests: - self.move_One(self.testdir) - - def update_tests(self,ourdir): - for xmlf in self.ourxmls: - capture = self.call_planemo(xmlf,ourdir) - logf = open(f"%s_run_report" % (self.tool_name),'w') - logf.write("stdout:") - logf.write(capture.stdout) - logf.write("stderr:") - logf.write(capture.stderr) - - class ToolConfUpdater(): # update config/tool_conf.xml with a new tool unpacked in /tools # requires highly insecure docker settings - like write to tool_conf.xml and to tools ! # if in a container possibly not so courageous. # Fine on your own laptop but security red flag for most production instances - def __init__(self, args, tool_conf_path, new_tool_archive_path, new_tool_name, tool_dir): + def __init__(self, args, tool_conf_path, new_tool_archive_path, new_tool_name, tool_dir): self.args = args - self.tool_conf_path = tool_conf_path + self.tool_conf_path = os.path.join(args.galaxy_root,tool_conf_path) + self.tool_dir = os.path.join(args.galaxy_root, tool_dir) self.our_name = 'ToolFactory' tff = tarfile.open(new_tool_archive_path, "r:*") flist = tff.getnames() ourdir = os.path.commonpath(flist) # eg pyrevpos self.tool_id = ourdir # they are the same for TF tools ourxml = [x for x in flist if x.lower().endswith('.xml')] - res = tff.extractall(tool_dir) + res = tff.extractall() tff.close() + self.run_rsync(ourdir, self.tool_dir) self.update_toolconf(ourdir,ourxml) + def run_rsync(self, srcf, dstf): + src = os.path.abspath(srcf) + dst = os.path.abspath(dstf) + if os.path.isdir(src): + cll = ['rsync', '-vr', src, dst] + else: + cll = ['rsync', '-v', src, dst] + p = subprocess.run( + cll, + capture_output=False, + encoding='utf8', + shell=False, + ) + def install_deps(self): gi = galaxy.GalaxyInstance(url=self.args.galaxy_url, key=self.args.galaxy_api_key) x = gi.tools.install_dependencies(self.tool_id) @@ -217,7 +112,9 @@ def update_toolconf(self,ourdir,ourxml): # path is relative to tools updated = False - tree = ET.parse(self.tool_conf_path) + localconf = './local_tool_conf.xml' + self.run_rsync(self.tool_conf_path,localconf) + tree = ET.parse(localconf) root = tree.getroot() hasTF = False TFsection = None @@ -235,7 +132,9 @@ updated = True ET.SubElement(TFsection, 'tool', {'file':xml}) ET.indent(tree) - tree.write(self.tool_conf_path, pretty_print=True) + newconf = f"{self.tool_id}_conf" + tree.write(newconf, pretty_print=True) + self.run_rsync(newconf,self.tool_conf_path) if False and self.args.packages and self.args.packages > '': self.install_deps() @@ -1171,8 +1070,8 @@ a("--include_tests", default=False, action="store_true") a("--install", default=False, action="store_true") a("--run_test", default=False, action="store_true") - a("--local_tools", default='tools') # relative to galaxy_root - a("--tool_conf_path", default='/galaxy_root/config/tool_conf.xml') + a("--local_tools", default='tools') # relative to $__root_dir__ + a("--tool_conf_path", default='config/tool_conf.xml') # relative to $__root_dir__ a("--galaxy_url", default="http://localhost:8080") a("--toolshed_url", default="http://localhost:9009") # make sure this is identical to tool_sheds_conf.xml @@ -1203,8 +1102,8 @@ tt = ToolTester(report_dir=r.repdir, in_tool_archive=r.newtarpath, new_tool_archive=r.args.new_tool, galaxy_root=args.galaxy_root, include_tests=False) if args.install: #try: - tcu = ToolConfUpdater(args=args, tool_dir=os.path.join(args.galaxy_root,args.local_tools), - new_tool_archive_path=r.newtarpath, tool_conf_path=os.path.join(args.galaxy_root,'config','tool_conf.xml'), + tcu = ToolConfUpdater(args=args, tool_dir=args.local_tools, + new_tool_archive_path=r.newtarpath, tool_conf_path=args.tool_conf_path, new_tool_name=r.tool_name) #except Exception: # print("### Unable to install the new tool. Are you sure you have all the required special settings?")
--- a/toolfactory/ToolFactory.xml Mon Apr 26 05:25:26 2021 +0000 +++ b/toolfactory/ToolFactory.xml Tue Apr 27 23:33:49 2021 +0000 @@ -196,6 +196,7 @@ <requirements> <requirement type="package" version="0.4.14">galaxyxml</requirement> <requirement type="package" version="0.15.0">bioblend</requirement> + <requirement type="package" version="3.2.3">rsync</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/toolfactory/ToolFactory_tester.py Mon Apr 26 05:25:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,202 +0,0 @@ -# see https://github.com/fubar2/toolfactory -# -# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 -# -# all rights reserved -# Licensed under the LGPL -# suggestions for improvement and bug fixes welcome at -# https://github.com/fubar2/toolfactory -# -# July 2020: BCC was fun and I feel like rip van winkle after 5 years. -# Decided to -# 1. Fix the toolfactory so it works - done for simplest case -# 2. Fix planemo so the toolfactory function works -# 3. Rewrite bits using galaxyxml functions where that makes sense - done - -import argparse -import copy -import os -import subprocess -import shutil -import sys -import tarfile -import tempfile -import time - -myversion = "V2.2 April 2021" -verbose = True -debug = True -toolFactoryURL = "https://github.com/fubar2/toolfactory" - -def timenow(): - """return current time as a string""" - return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time())) - -class ToolTester(): - # requires highly insecure docker settings - like write to tool_conf.xml and to tools ! - # if in a container possibly not so courageous. - # Fine on your own laptop but security red flag for most production instances - # uncompress passed tar, run planemo and rebuild a new tarball with tests - - def __init__(self, args=None, in_tool_archive='/galaxy-central/tools/newtool/newtool_toolshed.gz', new_tool_archive=None): - self.args = args - self.new_tool_archive = new_tool_archive - assert tarfile.is_tarfile(in_tool_archive) - # this is not going to go well with arbitrary names. TODO introspect tool xml! - self.tooloutdir = "./tfout" - self.repdir = "./TF_run_report" - self.testdir = os.path.join(self.tooloutdir, "test-data") - if not os.path.exists(self.tooloutdir): - os.mkdir(self.tooloutdir) - if not os.path.exists(self.testdir): - os.mkdir(self.testdir) - if not os.path.exists(self.repdir): - os.mkdir(self.repdir) - tff = tarfile.open(in_tool_archive, "r:*") - flist = tff.getnames() - ourdir = os.path.commonpath(flist) # eg pyrevpos - self.tool_name = ourdir - ourxmls = [x for x in flist if x.lower().endswith('.xml') and os.path.split(x)[0] == ourdir] - assert len(ourxmls) > 0 - self.ourxmls = ourxmls # [os.path.join(tool_path,x) for x in ourxmls] - res = tff.extractall() - tff.close() - self.update_tests(ourdir) - self.makeTool() - self.moveRunOutputs() - self.makeToolTar() - - def call_planemo(self,xmlpath,ourdir): - penv = os.environ - penv['HOME'] = '/home/ross/galaxy-release_21.01' - toolfile = os.path.split(xmlpath)[1] - tool_name = self.tool_name - tool_test_output = f"{tool_name}_planemo_test_report.html" - cll = [ - "planemo", - "test", - "--test_output", - os.path.abspath(tool_test_output), - "--galaxy_root", - self.args.galaxy_root, - "--update_test_data", - os.path.abspath(xmlpath), - ] - print(cll) - p = subprocess.run( - cll, - capture_output=True, - encoding='utf8', - env = penv, - shell=False, - ) - return p - - def makeTool(self): - """write xmls and input samples into place""" - for xreal in self.ourxmls: - x = os.path.split(xreal)[1] - xout = os.path.join(self.tooloutdir,x) - shutil.copyfile(xreal, xout) - # for p in self.infiles: - # pth = p["name"] - # dest = os.path.join(self.testdir, "%s_sample" % p["infilename"]) - # shutil.copyfile(pth, dest) - # dest = os.path.join(self.repdir, "%s_sample" % p["infilename"]) - # shutil.copyfile(pth, dest) - - def makeToolTar(self): - """move outputs into test-data and prepare the tarball""" - excludeme = "_planemo_test_report.html" - - def exclude_function(tarinfo): - filename = tarinfo.name - return None if filename.endswith(excludeme) else tarinfo - - newtar = 'new_%s_toolshed.gz' % self.tool_name - ttf = tarfile.open(newtar, "w:gz") - ttf.add(name=self.tooloutdir, - arcname=self.tool_name, - filter=exclude_function) - ttf.close() - shutil.copyfile(newtar, self.new_tool_archive) - - def moveRunOutputs(self): - """need to move planemo or run outputs into toolfactory collection""" - with os.scandir(self.tooloutdir) as outs: - for entry in outs: - if not entry.is_file(): - continue - if "." in entry.name: - _, ext = os.path.splitext(entry.name) - if ext in [".tgz", ".json"]: - continue - if ext in [".yml", ".xml", ".yaml"]: - newname = f"{entry.name.replace('.','_')}.txt" - else: - newname = entry.name - else: - newname = f"{entry.name}.txt" - dest = os.path.join(self.repdir, newname) - src = os.path.join(self.tooloutdir, entry.name) - shutil.copyfile(src, dest) - with os.scandir('.') as outs: - for entry in outs: - if not entry.is_file(): - continue - if "." in entry.name: - _, ext = os.path.splitext(entry.name) - if ext in [".yml", ".xml", ".yaml"]: - newname = f"{entry.name.replace('.','_')}.txt" - else: - newname = entry.name - else: - newname = f"{entry.name}.txt" - dest = os.path.join(self.repdir, newname) - src =entry.name - shutil.copyfile(src, dest) - if True or self.args.include_tests: - with os.scandir(self.testdir) as outs: - for entry in outs: - if (not entry.is_file()) or entry.name.endswith( - "_planemo_test_report.html" - ): - continue - if "." in entry.name: - _, ext = os.path.splitext(entry.name) - if ext in [".tgz", ".json"]: - continue - if ext in [".yml", ".xml", ".yaml"]: - newname = f"{entry.name.replace('.','_')}.txt" - else: - newname = entry.name - else: - newname = f"{entry.name}.txt" - dest = os.path.join(self.repdir, newname) - src = os.path.join(self.testdir, entry.name) - shutil.copyfile(src, dest) - - - def update_tests(self,ourdir): - for xmlf in self.ourxmls: - capture = self.call_planemo(xmlf,ourdir) - #sys.stderr.write('%s, stdout=%s, stderr=%s' % (xmlf, capture.stdout, capture.stdout)) - print('%s, stdout=%s, stderr=%s' % (capture.stdout, capture.stdout,xmlf)) - -def main(): - """ - This is a Galaxy wrapper. - It expects to be called by a special purpose tool.xml - - """ - parser = argparse.ArgumentParser() - a = parser.add_argument - a("--in_tool_archive", default=None) - a("--new_tested_tool_archive", default=None) - a("--galaxy_root", default="/home/ross/galaxy-release_21.01/") - args = parser.parse_args() - print('Hello from',os.getcwd()) - tt = ToolTester(args=args, in_tool_archive=args.in_tool_archive, new_tool_archive=args.new_tested_tool_archive) - -if __name__ == "__main__": - main()
--- a/toolfactory/install_tf_demos.py Mon Apr 26 05:25:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -import argparse -import urllib.request - -from bioblend import galaxy - -WF = "https://drive.google.com/uc?export=download&id=13xE8o7tucHGNA0qYkEP98FfUGl2wdOU5" -HIST = ( - "https://drive.google.com/uc?export=download&id=1V0ZN9ZBuqcGJvt2AP7s3g0q11uYEhdDB" -) -WF_FILE = "tf_workflow.ga" -HIST_FILE = "tf_history.tgz" - - -def _parser(): - parser = argparse.ArgumentParser() - parser.add_argument( - "-g", "--galaxy", help="URL of target galaxy", default="http://localhost:9090" - ) - parser.add_argument("-a", "--key", help="Galaxy admin key", default=None) - return parser - - -def main(): - """ - load the planemo tool_factory demonstration history and tool generating workflow - fails in planemo served galaxies because there seems to be no user in trans? - """ - args = _parser().parse_args() - urllib.request.urlretrieve(WF, WF_FILE) - urllib.request.urlretrieve(HIST, HIST_FILE) - assert args.key, "Need an administrative key for the target Galaxy supplied please" - gi = galaxy.GalaxyInstance( - url=args.galaxy, key=args.key, email="planemo@galaxyproject.org" - ) - x = gi.workflows.import_workflow_from_local_path(WF_FILE, publish=True) - print(f"installed {WF_FILE} Returned = {x}\n") - x = gi.histories.import_history(file_path=HIST_FILE) - print(f"installed {HIST_FILE} Returned = {x}\n") - - -if __name__ == "__main__": - main()
--- a/toolfactory/maketf.sh Mon Apr 26 05:25:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -# if a new ubuntu image, will need a port mapped and add some basics first -# apt update ; apt install -y python3-dev python3-venv python3-wheel nano curl wget git python3-setuptools -TARGDIR="/galaxy-central" -PDIR="/planemo" -git clone --recursive https://github.com/fubar2/planemo.git $PDIR -mkdir -p $TARGDIR -curl -L -s https://github.com/galaxyproject/galaxy/archive/dev.tar.gz | tar xzf - --strip-components=1 -C $TARGDIR -cd $PDIR -mkdir mytools -python3 -m venv .venv -. .venv/bin/activate -python3 setup.py build -python3 setup.py install -planemo conda_init --conda_prefix $PDIR/con -/planemo/con/bin/conda init -. ~/.bashrc -/planemo/con/bin/conda activate base -/planemo/con/bin/conda install -y -c bioconda -c conda-forge configparser galaxyxml -# without this, planemo does not work in docker... No clue why but planemo goes all pear shaped -# but pip reports that it's missing - installing it explicitly seems to do some kind of magic -echo "Starting first run. This takes ages and includes building the Galaxy client. Be patient. Do something else for 20 minutes" -. $PDIR/.venv/bin/activate -planemo tool_factory --galaxy_root $TARGDIR --port 9090 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install -# planemo tool_factory --galaxy_root $TARGDIR --port 8080 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install -#planemo tool_factory --galaxy_root $TARGDIR --conda_prefix $PDIR/con --port 9090 --host 0.0.0.0 -# planemo serve --galaxy_root /galaxy-central/ --conda_prefix /planemo/con --port 8080 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install /planemo/.venv/lib/python3.8/site-packages/planemo-0.74.1-py3.8.egg/planemo_ext/tool_factory_2 -# planemo serve --galaxy_root /galaxy-central/ --port 8080 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install /planemo/.venv/lib/python3.8/site-packages/planemo-0.74.1-py3.8.egg/planemo_ext/tool_factory_2 -# planemo serve --galaxy_root $TARGDIR --port 8080 --host 0.0.0.0 --conda_dependency_resolution --conda_auto_install /usr/local/lib/python3.6/dist-packages/planemo-0.74.1-py3.6.egg/planemo_ext/tool_factory_2/ - -# host is needed to get -p 9090:9090 to work in docker. Default 127.0.0.1 doesn't redirect :(ls -l /tmp
--- a/toolfactory/test-data/test1_log.txt Mon Apr 26 05:25:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -## Executing Toolfactory generated command line = python /tmp/pyrevposq5dmcdy1.python /tmp/tmpqrksf8sd/files/5/b/9/dataset_5b952a86-87df-44ad-a415-ea549f3f0cee.dat output2
--- a/toolfactory/tfout/.shed.yml Mon Apr 26 05:25:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -category: TF Generated Tools -description: Makes random plots -name: plotter -owner: planemo -synopsis: Makes random plots -type: unrestricted
--- a/toolfactory/tfout/plotter.xml Mon Apr 26 05:25:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -<tool name="plotter" id="plotter" version="0.01"> - <!--Source in git at: https://github.com/fubar2/toolfactory--> - <!--Created by planemo@galaxyproject.org at 31/03/2021 10:58:49 using the Galaxy Tool Factory.--> - <description>Makes random plots</description> - <requirements> - <requirement version="" type="package">r-base</requirement> - </requirements> - <stdio> - <exit_code range="1:" level="fatal"/> - </stdio> - <expand macro="stdio"/> - <version_command><![CDATA[echo "0.01"]]></version_command> - <command><![CDATA[Rscript -$runme -"$nplot"]]></command> - <configfiles> - <configfile name="runme"><![CDATA[ -\# demo -args = commandArgs(trailingOnly=TRUE) -if (length(args)==0) { - n_plots = 3 -} else { - n_plots = as.integer(args[1]) } -dir.create('plots') -for (i in 1:n_plots) { - foo = runif(100) - bar = rnorm(100) - bar = foo + 0.05*bar - pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_')) - plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6) - dev.off() - foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) - bar = as.matrix(foo) - pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_')) - heatmap(bar,main='Random Heatmap') - dev.off() -} - -]]></configfile> - </configfiles> - <inputs> - <param name="nplot" type="text" value="3" label="Number of random plots pairs to draw" help=""/> - </inputs> - <outputs> - <collection name="plots" type="list" label="Plots"> - <discover_datasets pattern="__name_and_ext__" directory="plots" visible="false"/> - </collection> - </outputs> - <tests> - <test> - <param name="nplot" value="3"/> - <output_collection name="plots"/> - </test> - </tests> - <help><![CDATA[ - -**What it Does** - -Makes plots into a collection demonstration - - - ------- - - -Script:: - - # demo - args = commandArgs(trailingOnly=TRUE) - if (length(args)==0) { - n_plots = 3 - } else { - n_plots = as.integer(args[1]) } - dir.create('plots') - for (i in 1:n_plots) { - foo = runif(100) - bar = rnorm(100) - bar = foo + 0.05*bar - pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_')) - plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6) - dev.off() - foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) - bar = as.matrix(foo) - pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_')) - heatmap(bar,main='Random Heatmap') - dev.off() - } - -]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/bts573</citation> - </citations> -</tool> -