# HG changeset patch # User fubar # Date 1597753543 14400 # Node ID f8700bed1e17185cfbed1fb2eb7676b524cf283d # Parent 668c37cc8962da348fe0ae25b4071e5c3e5ee9bc Uploaded diff -r 668c37cc8962 -r f8700bed1e17 toolfactory/docker/Dockerfile --- a/toolfactory/docker/Dockerfile Sun Aug 16 20:05:19 2020 -0400 +++ b/toolfactory/docker/Dockerfile Tue Aug 18 08:25:43 2020 -0400 @@ -3,44 +3,50 @@ # VERSION 0.2 # patches startup so the below will install a workflow dropped into $GALAXY_ROOT/workflows # use docker run -p 8080:80 -d -e GALAXY_AUTO_UPDATE_WORKFLOWS=/galaxy-central/workflows/TF_sample_wf.ga -v /home/ubuntu/galaxy_storage/:/export/ toolfactory -FROM bgruening/galaxy-stable +FROM quay.io/bgruening/galaxy:20.05 MAINTAINER Ross Lazarus ross.lazarus@gmail.com ENV GALAXY_CONFIG_BRAND=ToolFactory ENV GALAXY_LOGGING="full" - -# RUN apt-get update -y && apt-get install -y build-essential gcc apt-utils -# needed for planemo build - -RUN /galaxy_venv/bin/python -m pip install --upgrade pip -# RUN /galaxy_venv/bin/python -m pip install planemo - +ADD tfwelcome.html /export/welcome.html # RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed' -ADD my_tool_list.yml $GALAXY_ROOT/config/toolfactory_tools.yaml -ENV GALAXY_AUTO_UPDATE_TOOLS=$GALAXY_ROOT/config/toolfactory_tools.yaml +RUN mkdir -p /tftools \ + && mkdir -p /tftools/toolfactory \ + && mkdir -p /tftools/planemo_test + +ADD ./tftools/toolfactory /tftools/toolfactory +ADD ./tftools/tf_tool_conf.xml /tftools/tf_tool_conf.xml +ADD ./tftools/planemo_test /tftools/planemo_test +ADD TF_example_wf.ga /tftools/TF_example_wf.ga +ADD my_tool_list.yml /tftools/toolfactory_tools.yaml + +ENV GALAXY_AUTO_UPDATE_TOOLS=/tftools/toolfactory_tools.yaml +# NOTE above does work but takes 1-2 minutes + +# ENV GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/tf_tool_conf.xml,config/shed_tool_conf.xml.sample +#ENV GALAXY_CONFIG_TOOL_CONFIG_FILE=/tftools/tf_tool_conf.xml,config/tool_conf.xml.sample +# works but does not install dependencies # Add workflows to the Docker image -RUN mkdir -p $GALAXY_ROOT/workflows -ADD TF_example_wf.ga $GALAXY_ROOT/workflows/TF_example_wf.ga + +ENV $GALAXY_DEFAULT_ADMIN_USER="admin" +# ensure triggering post-start-actions.sh + +ADD tftools/datatypes_conf.xml $GALAXY_ROOT/conf/datatypes_conf.xml.sample ADD post-start-actions.sh /export/post-start-actions.sh +ADD post-start-actions.sh $GALAXY_ROOT/config/post-start-actions.sh + RUN chmod a+xr /export/post-start-actions.sh \ - && chmod a+xr $GALAXY_ROOT/workflows/TF_example_wf.ga - + && chmod a+xr /tftools/TF_example_wf.ga \ + && chmod a+xr $GALAXY_ROOT/config/post-start-actions.sh # Add Galaxy interactive tours # ADD ./rna-workbench-tours/* $GALAXY_ROOT/config/plugins/tours/ # Add data library definition file # ADD library_data.yaml $GALAXY_ROOT/library_data.yaml -# cleanup dance -RUN apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \ - && find $GALAXY_ROOT/ -name '*.pyc' -delete | true \ - && find /usr/lib/ -name '*.pyc' -delete | true \ - && find /var/log/ -name '*.log' -delete | true \ - && find $GALAXY_VIRTUAL_ENV -name '*.pyc' -delete | true \ - && rm -rf /tmp/* /root/.cache/ /var/cache/* $GALAXY_ROOT/client/node_modules/ $GALAXY_VIRTUAL_ENV/src/ /home/galaxy/.cache/ /home/galaxy/.npm -ENV GALAXY_DEFAULT_ADMIN_USER='' -VOLUME ["/export/"] + +VOLUME ["/export/", "/data/", "/var/lib/docker"] EXPOSE :80 EXPOSE :21 EXPOSE :8800 + CMD ["/usr/bin/startup"] - diff -r 668c37cc8962 -r f8700bed1e17 toolfactory/docker/postinstall.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/postinstall.py Tue Aug 18 08:25:43 2020 -0400 @@ -0,0 +1,6 @@ +from bioblend import galaxy + +gi = galaxy.GalaxyInstance(url='http://127.0.0.1:8080', key='fbdd3c2eecd191e88939fffc02eeeaf8') + +hl = gi.histories.get_histories() +h = get_most_recently_used_history() diff -r 668c37cc8962 -r f8700bed1e17 toolfactory/docker/tfwelcome.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/tfwelcome.html Tue Aug 18 08:25:43 2020 -0400 @@ -0,0 +1,61 @@ + + + + + + + + +
+
+
+

Hello, your Galaxy ToolFactory Docker container is running!

+ If you have not already done so, + From a handy linux console, please use
+ docker ps
+ to find this container's name then use
+ docker exec [container name] config/post-start-actions.sh +
+ to load the sample tool generators to fully populate this container. + until the Dockerfile for this container figures out how to load a workflow during the build correctly.
+ To run the workflow you need two small datasets until I get them loaded
+ phiX.fasta from the Galaxy test-sample directory, and any smallish text file you want such as a readme or script.
+ When you run the workflow, feed the fasta where it says, and the text file where you see rgToolFactory.py
+ Send it to the same history and let it run.
+ With any luck, you will have a history of examples to play with - use the rerun button to repopulate the ToolFactory form to illustrate
+ positional and argparse style parameter passing for python, a simple bash script using STDIN/STDOUT and the perl (ugh) example from planemo
+ Configuring Galaxy » + Installing Tools » + Guided Tour » + 		+
+ +
+ +
+
+
+ +
+ +

+ + Galaxy is an open platform for supporting data intensive + research. Galaxy is developed by The Galaxy Team + with the support of many contributors. + The Galaxy Docker project is supported by the University of Freiburg, part of de.NBI. +

+ + + +
+ + + diff -r 668c37cc8962 -r f8700bed1e17 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Sun Aug 16 20:05:19 2020 -0400 +++ b/toolfactory/rgToolFactory2.py Tue Aug 18 08:25:43 2020 -0400 @@ -173,10 +173,17 @@ self.testparam = [] if ( self.args.runmode == "Executable" or self.args.runmode == "system" - ): # binary - no need - aCL(self.args.exe_package) # this little CL will just run + ): + if len(self.args.cl_override) > 0: + for x in self.args.cl_override.split(' '): + aCL(x) + else: + aCL(self.args.exe_package) # this little CL will just run else: self.prepScript() + aCL(self.args.interpreter_name) + aCL(self.sfile) + self.elog = "%s_error_log.txt" % self.tool_name self.tlog = "%s_runner_log.txt" % self.tool_name @@ -231,7 +238,6 @@ self.clargparse() def prepScript(self): - aCL = self.cl.append rx = open(self.args.script_path, "r").readlines() rx = [x.rstrip() for x in rx] rxcheck = [x.strip() for x in rx if x.strip() > ""] @@ -255,9 +261,9 @@ artifact.write(bytes("#!/usr/bin/env python\n", "utf8")) artifact.write(bytes(self.script, "utf8")) artifact.close() - aCL(self.args.interpreter_name) - aCL(self.sfile) - + + + def cleanuppar(self): """ positional parameters are complicated by their numeric ordinal""" for i, p in enumerate(self.infiles): @@ -482,7 +488,10 @@ Uses galaxyhtml Hmmm. How to get the command line into correct order... """ - self.tool.command_line_override = self.xmlcl + if self.args.cl_override: + self.tool.command_line_override = self.args.cl_override.split(' ') + self.xmlcl + else: + self.tool.command_line_override = self.xmlcl if self.args.interpreter_name: self.tool.interpreter = self.args.interpreter_name if self.args.help_text: @@ -499,6 +508,13 @@ requirements = gxtp.Requirements() if self.args.interpreter_name: + if self.args.dependencies: + for d in self.args.dependencies.split(','): + requirements.append( + gxtp.Requirement( + "package", d, "" + ) + ) if self.args.interpreter_name == "python": requirements.append( gxtp.Requirement( @@ -691,6 +707,8 @@ parser = argparse.ArgumentParser() a = parser.add_argument a("--script_path", default="") + a("--dependencies", default="") + a("--cl_override", default="") a("--tool_name", default=None) a("--interpreter_name", default=None) a("--interpreter_version", default=None) diff -r 668c37cc8962 -r f8700bed1e17 toolfactory/rgToolFactory2.xml --- a/toolfactory/rgToolFactory2.xml Sun Aug 16 20:05:19 2020 -0400 +++ b/toolfactory/rgToolFactory2.xml Tue Aug 18 08:25:43 2020 -0400 @@ -92,10 +92,11 @@ - - + + + + + @@ -106,10 +107,12 @@ + + + + - @@ -131,10 +134,14 @@ $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__ #else: $__tool_directory__/rgToolFactory2.py +--dependencies "$interexe.dependencies" --runmode "$interexe.interpreter" + #if len(str($interexe.cl_override)) > 0: +--cl_override "$interexe.cl_override" + #end if #if str($interexe.interpreter)=="Executable" or str($interexe.interpreter)=="system": --exe_package="$interexe.exe_package" - #if str($interexe.exe_package_version) != 'None' : + #if $interexe.exe_package_version: --exe_package_version="$interexe.exe_package_version" #end if #else: @@ -159,12 +166,9 @@ --additional_parameters="$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed" #end for #end if - #for $intab in $ppass.history_inputs: --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help" #end for - - #for $otab in $ppass.history_outputs: --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL" #end for @@ -220,16 +224,19 @@ - + + - - + + + + @@ -246,9 +253,6 @@ - - -