Mercurial > repos > mvdbeek > docker_scriptrunner
changeset 0:b6211faea403 draft
planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
| author | mvdbeek |
|---|---|
| date | Fri, 08 Jul 2016 15:09:10 -0400 |
| parents | |
| children | 29adb7607591 |
| files | README.txt dockerfiles/r-bioperl-python/Dockerfile dockerfiles/scriptrunner/Dockerfile macros.xml planemo_serve_script.sh scriptrunner.py scriptrunner.xml test-data/docker_images.loc.sample tool-data/docker_images.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.sample.test tool_dependencies.xml |
| diffstat | 12 files changed, 1126 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,311 @@ +# WARNING before you start +# Carefully inspect tool usage. If bugs are found within the tool, users may be able to break +# out of the container and mount files on the host system. + +This is a fork of toolfactory that makes use of Docker to sandbox the generated script. +As such you need to have the system user under which galaxy tools are executed be able to run Docker. +On Ubuntu you can do this by adding your galaxy user to the docker group (http://askubuntu.com/questions/477551/how-can-i-use-docker-without-sudo). +Assuming galaxy runs as the user galaxy, this is the short form for installing Docker from the official docker Ubuntu Trusty repository: + +sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 36A1D7869245C8950F966E92D8576A8BA88D21E9 +sudo sh -c "echo deb https://get.docker.io/ubuntu docker main > /etc/apt/sources.list.d/docker.list" +sudo apt-get update +sudo apt-get install lxc-docker +sudo gpasswd -a galaxy docker +sudo service docker restart + +Eventually the galaxy process might need to be restarted. + +On OSX, you need to boot2docker installed and available to the galaxy user. + +Note that this could bring severe security problems in case untrusted users can become this user. +If you want to use this tool, read and understand the following article: +https://docs.docker.com/articles/security/#docker-daemon-attack-surface + +Work is ongoing, some important features are missing, like being able to manage containers. +Currently, only a single container with pre-installed tools is available. + +This is an beta-stage, potentially dangerous tool. + +Please cite: + - http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref + - van den Beek M., Antoniewski C., in preparation +if you use this tool in your published work. + +*Short Story* + +This is an unusual Galaxy tool that exposes unrestricted scripting to users of a Galaxy server, +allowing them to run scripts in R, python, sh and perl over input datasets, +writing a single new data set as output. + +In addition, this tool optionally generates very simple new Galaxy tools, that effectively +freeze the supplied script into a new, ordinary Galaxy tool that runs it over one or more input files, +working just like any other Galaxy tool for your users. + +To use the ToolFactory, you should have prepared a script to paste into a text box, +and a small test input example ready to select from your history to test your new script. +There is an example in each scripting language on the Tool Factory form. You can just +cut and paste these to try it out - remember to select the right interpreter please. You'll +also need to create a small test data set using the Galaxy history add new data tool. + +If the script fails somehow, use the "redo" button on the tool output in your history to +recreate the form complete with broken script. Fix the bug and execute again. Rinse, wash, repeat. + +Once the script runs sucessfully, a new Galaxy tool that runs your script can be generated. +Select the "generate" option and supply some help text and names. The new tool will be +generated in the form of a new Galaxy datatype - toolshed.gz - as the name suggests, +it's an archive ready to upload to a Galaxy ToolShed as a new tool repository. + +Once it's in a ToolShed, it can be installed into any local Galaxy server from +the Galaxy administrative interface. + +Once the new tool is installed, local users can run it - each time, the script that was supplied +when it was built will be executed with the input chosen from the user's history. In other words, +the tools you generate with the ToolFactory run just like any other Galaxy tool, +but run your script every time. + +Tool factory tools are perfect for workflow components. One input, one output, no variables. + +*Reasons to read further* + +If you use Galaxy to support your research; + +You and fellow users are sometimes forced to take data out of Galaxy, process it with ugly +little perl/awk/sed/R... scripts and put it back; + +You do this when you can't do some transformation in Galaxy (the 90/10 rule); + +You don't have enough developer resources for wrapping dozens of even relatively simple tools; + +Your research and your institution would be far better off if those feral scripts were all tucked +safely in your local toolshed and Galaxy histories. + +*The good news* If it can be trivially scripted, it can be running safely in your +local Galaxy via your own local toolshed in a few minutes - with functional tests. + + +*Value proposition* The ToolFactory allows Galaxy to efficiently take over most of your lab's +dark script matter, making it reproducible in Galaxy and shareable through the ToolShed. + +That's what this tool does. You paste a simple script and the tool returns +a new, real Galaxy tool, ready to be installed from the local toolshed to local servers. +Scripts can be wrapped and online literally within minutes. + +*To fully and safely exploit the awesome power* of this tool, Galaxy and the ToolShed, +you should be a developer installing this tool on a private/personal/scratch local instance where you +are an admin_user. Then, if you break it, you get to keep all the pieces +see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home + +** Installation ** +This is a Galaxy tool. You can install it most conveniently using the administrative "Search and browse tool sheds" link. +Find the Galaxy Test toolshed (not main) and search for the toolfactory repository. +Open it and review the code and select the option to install it. + +If you can't get the tool that way, the xml and py files here need to be copied into a new tools +subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry pointing to the xml +file - something like:: + + <section name="Tool building tools" id="toolbuilders"> + <tool file="DockerToolFactory.xml"/> + </section> + +If not already there (I just added it to datatypes_conf.xml.sample), please add: +<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> +to your local data_types_conf.xml. + +Ensure that html sanitization is set to False and uncommented in universe_wsgi.ini + +You'll have to restart the server for the new tool to be available. + +R, python, perl are preloaded in the supplied Dockerfile. +Upon first execution the Dockerfile will be used to build an image +with varius pre-installed tools. +Adding new ones should be easy enough, and follows standard conventions +for Docker tools. +Please make suggestions as bitbucket issues and code. +The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick . + +*What it does* This is a tool factory for simple scripts in python, R and perl currently. +Functional tests are automatically generated. +On a technical level, a Docker container is started, and input and output files +are made available to the container. +After running, the docker container will be terminated. + +LIMITED to simple scripts that read inputs from the history. +Optionally can write one new history dataset, and optionally collect any number of outputs into links on an autogenerated HTML +index page for the user to navigate - useful if the script writes images and output files - pdf outputs +are shown as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and imagemagik need to +be avaailable. + +Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up since +a generated script gets you a serious leg up to a more complex one. + +*What you do* You paste and run your script +you fix the syntax errors and eventually it runs +You can use the redo button and edit the script before +trying to rerun it as you debug - it works pretty well. + +Once the script works on some test data, you can +generate a toolshed compatible gzip file +containing your script ready to run as an ordinary Galaxy tool in a +repository on your local toolshed. That means safe and largely automated installation in any +production Galaxy configured to use your toolshed. + +*Generated tool Security* Once you install a generated tool, it's just +another tool - assuming the script is safe. They just run normally and their user cannot do anything unusually insecure +but please, practice safe toolshed. +Read the fucking code before you install any tool. +Especially this one - it is really scary. + +If you opt for an HTML output, you get all the script outputs arranged +as a single Html history item - all output files are linked, thumbnails for all the pdfs. +Ugly but really inexpensive. + +Patches and suggestions welcome as bitbucket issues please? + + +copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 + +all rights reserved +Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home + +Material for our more enthusiastic and voracious readers continues below - we salute you. + +**Motivation** Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs +- even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible. + +**Benefits** For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics +tasks. Once a user has a working R (or python or perl) script that does something Galaxy cannot currently do (eg transpose a +tabular file) and takes parameters the way Galaxy supplies them (see example below), they: + +1. Install the tool factory on a personal private instance + +2. Upload a small test data set + +3. Paste the script into the 'script' text box and iteratively run the insecure tool on test data until it works right - +there is absolutely no reason to do this anywhere other than on a personal private instance. + +4. Once it works right, set the 'Generate toolshed gzip' option and run it again. + +5. A toolshed style gzip appears ready to upload and install like any other Toolshed entry. + +6. Upload the new tool to the toolshed + +7. Ask the local admin to check the new tool to confirm it's not evil and install it in the local production galaxy + +**Simple examples on the tool form** + +A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, +does something (transpose in this case) and writes the results to a new tabular file:: + + # transpose a tabular input file and write as a tabular output file + ourargs = commandArgs(TRUE) + inf = ourargs[1] + outf = ourargs[2] + inp = read.table(inf,head=F,row.names=NULL,sep='\t') + outp = t(inp) + write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F) + +Calculate a multiple test adjusted p value from a column of p values - for this script to be useful, +it needs the right column for the input to be specified in the code for the +given input file type(s) specified when the tool is generated :: + + # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use + column = 1 # adjust if necessary for some other kind of input + fdrmeth = 'BH' + ourargs = commandArgs(TRUE) + inf = ourargs[1] + outf = ourargs[2] + inp = read.table(inf,head=T,row.names=NULL,sep='\t') + p = inp[,column] + q = p.adjust(p,method=fdrmeth) + newval = paste(fdrmeth,'p-value',sep='_') + q = data.frame(q) + names(q) = newval + outp = cbind(inp,newval=q) + write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T) + + + +Another Rscript example without any input file - generates a random heatmap pdf - you must make sure the option to create an HTML output file is +turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page:: + + # note this script takes NO input or output because it generates random data + 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( "heattest.pdf" ) + heatmap(bar,main='Random Heatmap') + dev.off() + +A Python example that reverses each row of a tabular file. You'll need to remove the leading spaces for this to work if cut +and pasted into the script box. Note that you can already do this in Galaxy by setting up the cut columns tool with the +correct number of columns in reverse order,but this script will work for any number of columns so is completely generic:: + +# reverse order of columns in a tabular file +import sys +inp = sys.argv[1] +outp = sys.argv[2] +i = open(inp,'r') +o = open(outp,'w') +for row in i: + rs = row.rstrip().split('\t') + rs.reverse() + o.write('\t'.join(rs)) + o.write('\n') +i.close() +o.close() + + +Galaxy as an IDE for developing API scripts +If you need to develop Galaxy API scripts and you like to live dangerously, please read on. + +Galaxy as an IDE? +Amazingly enough, blend-lib API scripts run perfectly well *inside* Galaxy when pasted into a Tool Factory form. No need to generate a new tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously, it is actually quite useable. + +Why bother - what's wrong with Eclipse +Nothing. But, compared with developing API scripts in the usual way outside Galaxy, you get persistence and other framework benefits plus at absolutely no extra charge, a ginormous security problem if you share the history or any outputs because they contain the api script with key so development servers only please! + +Workflow +Fire up the Tool Factory in Galaxy. + +Leave the input box empty, set the interpreter to python, paste and run an api script - eg working example (substitute the url and key) below. + +It took me a few iterations to develop the example below because I know almost nothing about the API. I started with very simple code from one of the samples and after each run, the (edited..) api script is conveniently recreated using the redo button on the history output item. So each successive version of the developing api script you run is persisted - ready to be edited and rerun easily. It is ''very'' handy to be able to add a line of code to the script and run it, then view the output to (eg) inspect dicts returned by API calls to help move progressively deeper iteratively. + +Give the below a whirl on a private clone (install the tool factory from the main toolshed) and try adding complexity with few rerun/edit/rerun cycles. + +Eg tool factory api script +import sys +from blend.galaxy import GalaxyInstance +ourGal = 'http://x.x.x.x:xxxx' +ourKey = 'xxx' +gi = GalaxyInstance(ourGal, key=ourKey) +libs = gi.libraries.get_libraries() +res = [] +# libs looks like +# u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data', +for lib in libs: + res.append('%s:\n' % lib['name']) + res.append(str(gi.libraries.show_library(lib['id'],contents=True))) +outf=open(sys.argv[2],'w') +outf.write('\n'.join(res)) +outf.close() + +**Attribution** +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 + +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref + +**Licensing** +Copyright Ross Lazarus 2010 +ross lazarus at g mail period com + +All rights reserved. + +Licensed under the LGPL + +**Obligatory screenshot** + +http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dockerfiles/r-bioperl-python/Dockerfile Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,12 @@ +# Script runner base image +# +# VERSION 0.3 +# This Dockerfile is the base system for executing scripts with the docker scriptrunner. + +FROM mvdbeek/scriptrunner + +MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com + +RUN bash -c ". activate default && \ + conda install -y ncurses biopython perl-bioperl bedtools bioconductor-deseq2 bioconductor-edger numpy scipy" +CMD /bin/bash -c ". activate default && exec /bin/bash"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dockerfiles/scriptrunner/Dockerfile Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,34 @@ +# Script runner base image +# +# VERSION 0.3 +# This Dockerfile is the base system for executing scripts with the docker scriptrunner. + +FROM toolshed/requirements + +MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com + +# make sure the package repository is up to date +ENV DEBIAN_FRONTEND noninteractive +RUN apt-get -qq update + +# Install all requirements that are recommend by the Galaxy project +RUN apt-get install -y --no-install-recommends imagemagick libfreetype6-dev wget curl \ +libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev liblzma-dev \ +libpcre3-dev libbz2-dev libx11-dev + +RUN useradd galaxy --create-home --uid 1450 && \ + chown -R galaxy:galaxy /home/galaxy/ +USER galaxy +WORKDIR /home/galaxy +ENV CONDA_PREFIX="/home/galaxy/conda" \ + PATH="/home/galaxy/conda/envs/default/bin:/home/galaxy/conda/bin:$PATH" + +RUN curl https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -L -o miniconda.sh +RUN bash miniconda.sh -b -p "$CONDA_PREFIX" && rm miniconda.sh +RUN bash -c "conda create -y -q -c bioconda --name default samtools==0.1.19 bcftools && \ + conda config --add channels r && \ + conda config --add channels bioconda && \ + conda config --add channels iuc && \ + . activate default && \ + conda install ghostscript" +CMD /bin/bash -c ". activate default && exec /bin/bash"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,187 @@ + +<macro> + <xml name="help_macro"> + <help> +.. class:: warningmark + +**Details and attribution** Docker_toolfactory_ + +**If you find a bug** please raise an issue at the bitbucket repository Issues_ + +**What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy. + +**Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history. + +**Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs, +a new HTML report linking all the files and images created by the script can be automatically generated. + +.. class:: warningmark + +**Note to system administrators** This tool uses docker containers as protection against malicious scripts. It should only be installed on private/personnal Galaxy instances. + +.. class:: warningmark + +**Use on public servers** is STRONGLY discouraged for obvious reasons + +The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation. +We recommend that you follow the good code hygiene practices associated with safe toolshed. + +**Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not select one, and the path to the optional +output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below. +Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output. +This can be handy for complex scripts creating lots of output. + +**Examples** +<![CDATA[ + +Each of these following trivial examples can be cut and pasted into the script box for testing. +Please make sure you choose the appropriate interpreter and upload and select a suitable small matching test data input + +A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and +writes the results to a new tabular file. Note the use of colClasses to ensure that no fiddling takes place with numeric values by treating everything +as a string:: + + # transpose a tabular input file and write as a tabular output file + ourargs = commandArgs(TRUE) + inf = ourargs[1] + outf = ourargs[2] + inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character") + outp = t(inp) + write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F) + +Calculate a multiple test adjusted p value from a column of p values - for this script to be useful, it needs the right column for the input to be specified in the code for the +given input file type(s) specified when the tool is generated :: + + # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use + column = 1 # adjust if necessary for some other kind of input + ourargs = commandArgs(TRUE) + inf = ourargs[1] + outf = ourargs[2] + inp = read.table(inf,head=T,row.names=NULL,sep='\t') + p = inp[,column] + q = p.adjust(p,method='BH') + outp = cbind(inp,'BH Adjusted p-value'=q) + write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T) + + +A demonstration Rscript example takes no input file but generates some random data based pdf images +You must make sure the option to create an HTML output file is +turned on for this to work. Images (pdf) are linked via thumbnails and +all files have a link on the resulting HTML page:: + + # note this script takes NO input or output because it generates random data + for (i in 1:10) { + foo = runif(100) + bar = rnorm(100) + bar = foo + 0.05*bar + pdf(paste('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('yet',i,"anotherheatmap.pdf",sep='_')) + heatmap(bar,main='Random Heatmap') + dev.off() + } + +# A slight variation taking an input tabular file from which we read the first number as nreps +# his script takes a single parameter +# number of replicates + +.. code-block:: R + + ourargs = commandArgs(TRUE) + infname = ourargs[1] + nreps = read.table(infname,head=F) + nreps = unlist(nreps)[1] + nreps = max(c(1,nreps)) + nreps = min(c(20,nreps)) + print(paste("Using nreps=",nreps)) + for (i in 1:nreps) { + foo = runif(100) + bar = rnorm(100) + bar = foo + 0.2*bar + pdf(paste("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("yet",i,"anotherheatmap.pdf",sep="_")) + heatmap(bar,main="Random Heatmap") + dev.off() + } + +A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces +for this to work if cut and pasted into the script box):: + + # reverse order of columns in a tabular file + import sys + inp = sys.argv[1] + outp = sys.argv[2] + i = open(inp,'r') + o = open(outp,'w') + for row in i: + rs = row.rstrip().split('\t') + rs.reverse() + o.write('\t'.join(rs)) + o.write('\n') + i.close() + o.close() + +A trivial shell script example to show that it works:: + + #!/bin/bash + INF=$1 + OUTF=$2 + cut -c2,4,6,8,10,12 $INF > $OUTF + +A trivial perl script example to show that even perl works:: + + # + # change all occurances of a string in a file to another string + # + $oldfile = $ARGV[0]; + $newfile = $ARGV[1]; + $old = "gene"; + $new = "foo"; + open(OF, $oldfile); + open(NF, ">$newfile"); + # read in each line of the file + while ($line = <OF>) { + $line =~ s/$old/$new/; + print NF $line; + } + close(OF); + close(NF); + +]]> + +**Citation** + + +Paper_ : + +Creating re-usable tools from scripts: The Galaxy Tool Factory +Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + + +**Licensing** + +Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012 +All rights reserved. +Licensed under the LGPL_ + +.. _LGPL: http://www.gnu.org/copyleft/lesser.html +.. _Docker_toolfactory: https://bitbucket.org/mvdbeek/dockertoolfactory +.. _Issues: https://bitbucket.org/mvdbeek/dockertoolfactory/issues +.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref + + </help> +<citations> + <citation type="doi">10.1093/bioinformatics/bts573</citation> +</citations> + </xml> + <xml name="test_data_macro"> + </xml> +</macro>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_serve_script.sh Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,1 @@ +planemo serve --galaxy_branch dev --conda_prefix=/conda --conda_dependency_resolution --profile tf --port 80 --host 0.0.0.0 --job_config_file ~/mydisk/job_conf.xml --tool_data_table tool_data_table_conf.xml.sample.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scriptrunner.py Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,422 @@ +# DockerToolFactory.py +# see https://github.com/mvdbeek/scriptrunner + +import sys +import shutil +import subprocess +import os +import time +import tempfile +import argparse +import getpass +import tarfile +import re +import shutil +import math +import fileinput +from os.path import abspath + + +progname = os.path.split(sys.argv[0])[1] +verbose = False +debug = False + +def timenow(): + """return current time as a string + """ + return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) + +html_escape_table = { + "&": "&", + ">": ">", + "<": "<", + "$": "\$" + } + +def html_escape(text): + """Produce entities within text.""" + return "".join(html_escape_table.get(c,c) for c in text) + +def cmd_exists(cmd): + return subprocess.call("type " + cmd, shell=True, + stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0 + +def construct_bind(host_path, container_path=False, binds=None, ro=True): + #TODO remove container_path if it's alwyas going to be the same as host_path + '''build or extend binds dictionary with container path. binds is used + to mount all files using the docker-py client.''' + if not binds: + binds={} + if isinstance(host_path, list): + for k,v in enumerate(host_path): + if not container_path: + container_path=host_path[k] + binds[host_path[k]]={'bind':container_path, 'ro':ro} + container_path=False #could be more elegant + return binds + else: + if not container_path: + container_path=host_path + binds[host_path]={'bind':container_path, 'ro':ro} + return binds + +def switch_to_docker(opts): + import docker #need local import, as container does not have docker-py + current_user = getpass.getuser() + docker_client=docker.Client() + toolfactory_path=abspath(sys.argv[0]) + binds=construct_bind(host_path=opts.script_path, ro=False) + binds=construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False) + if len(opts.input_tab)>0: + binds=construct_bind(binds=binds, host_path=opts.input_tab, ro=True) + if not opts.output_tab == 'None': + binds=construct_bind(binds=binds, host_path=opts.output_tab, ro=False) + if opts.make_HTML: + binds=construct_bind(binds=binds, host_path=opts.output_html, ro=False) + binds=construct_bind(binds=binds, host_path=toolfactory_path) + volumes=binds.keys() + sys.argv=[abspath(opts.output_dir) if sys.argv[i-1]=='--output_dir' else arg for i,arg in enumerate(sys.argv)] ##inject absolute path of working_dir + cmd=['python', '-u']+sys.argv+['--dockerized', '1'] + container=docker_client.create_container( + image=opts.docker_image, # Make this configureable through job_conf + user=current_user, # TODO: make this configurable on the current user + volumes=volumes, + command=cmd + ) + docker_client.start(container=container[u'Id'], binds=binds) + docker_client.wait(container=container[u'Id']) + logs=docker_client.logs(container=container[u'Id']) + print "".join([log for log in logs]) + docker_client.remove_container(container[u'Id']) + +class ScriptRunner: + """class is a wrapper for an arbitrary script + """ + + def __init__(self,opts=None,treatbashSpecial=True, image_tag='base'): + """ + cleanup inputs, setup some outputs + + """ + self.opts = opts + self.scriptname = 'script' + self.useGM = cmd_exists('gm') + self.useIM = cmd_exists('convert') + self.useGS = cmd_exists('gs') + self.temp_warned = False # we want only one warning if $TMP not set + self.treatbashSpecial = treatbashSpecial + self.image_tag = image_tag + os.chdir(abspath(opts.output_dir)) + self.thumbformat = 'png' + s = open(self.opts.script_path,'r').readlines() + s = [x.rstrip() for x in s] # remove pesky dos line endings if needed + self.script = '\n'.join(s) + fhandle,self.sfile = tempfile.mkstemp(prefix='script',suffix=".%s" % (opts.interpreter)) + tscript = open(self.sfile,'w') # use self.sfile as script source for Popen + tscript.write(self.script) + tscript.close() + self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help + self.escapedScript = '\n'.join([html_escape(x) for x in s]) + self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.scriptname) + if opts.output_dir: # may not want these complexities + self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.scriptname) + art = '%s.%s' % (self.scriptname,opts.interpreter) + artpath = os.path.join(self.opts.output_dir,art) # need full path + artifact = open(artpath,'w') # use self.sfile as script source for Popen + artifact.write(self.script) + artifact.close() + self.cl = [] + self.html = [] + a = self.cl.append + a(opts.interpreter) + if self.treatbashSpecial and opts.interpreter in ['bash','sh']: + a(self.sfile) + else: + a('-') # stdin + for input in opts.input_tab: + a(input) + if opts.output_tab == 'None': #If tool generates only HTML, set output name to toolname + a(str(self.scriptname)+'.out') + a(opts.output_tab) + for param in opts.additional_parameters: + param, value=param.split(',') + a('--'+param) + a(value) + self.outFormats = opts.output_format + self.inputFormats = [formats for formats in opts.input_formats] + self.test1Input = '%s_test1_input.xls' % self.scriptname + self.test1Output = '%s_test1_output.xls' % self.scriptname + self.test1HTML = '%s_test1_output.html' % self.scriptname + + + def compressPDF(self,inpdf=None,thumbformat='png'): + """need absolute path to pdf + note that GS gets confoozled if no $TMP or $TEMP + so we set it + """ + assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) + hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'a') + our_env = os.environ.copy() + our_tmp = our_env.get('TMP',None) + if not our_tmp: + our_tmp = our_env.get('TEMP',None) + if not (our_tmp and os.path.exists(our_tmp)): + newtmp = os.path.join(self.opts.output_dir,'tmp') + try: + os.mkdir(newtmp) + except: + sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp) + our_env['TEMP'] = newtmp + if not self.temp_warned: + sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp) + self.temp_warned = True + outpdf = '%s_compressed' % inpdf + cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf] + x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval1 = x.wait() + sto.close() + if retval1 == 0: + os.unlink(inpdf) + shutil.move(outpdf,inpdf) + os.unlink(hlog) + hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'w') + outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) +# if self.useGM: +# cl2 = ['gm', 'convert', inpdf, outpng] +# else: # assume imagemagick + cl2 = ['convert', inpdf, outpng] + x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval2 = x.wait() + sto.close() + if retval2 == 0: + os.unlink(hlog) + retval = retval1 or retval2 + return retval + + + def getfSize(self,fpath,outpath): + """ + format a nice file size string + """ + size = '' + fp = os.path.join(outpath,fpath) + if os.path.isfile(fp): + size = '0 B' + n = float(os.path.getsize(fp)) + if n > 2**20: + size = '%1.1f MB' % (n/2**20) + elif n > 2**10: + size = '%1.1f KB' % (n/2**10) + elif n > 0: + size = '%d B' % (int(n)) + return size + + def makeHtml(self): + """ Create an HTML file content to list all the artifacts found in the output_dir + """ + + galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="toolFormBody"> + """ + galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" + galhtmlpostfix = """</div></body></html>\n""" + + flist = os.listdir(self.opts.output_dir) + flist = [x for x in flist if x <> 'Rplots.pdf'] + flist.sort() + html = [] + html.append(galhtmlprefix % progname) + html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.scriptname,timenow())) + fhtml = [] + if len(flist) > 0: + logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections + logfiles.sort() + logfiles = [x for x in logfiles if abspath(x) <> abspath(self.tlog)] + logfiles.append(abspath(self.tlog)) # make it the last one + pdflist = [] + npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) + for rownum,fname in enumerate(flist): + dname,e = os.path.splitext(fname) + sfsize = self.getfSize(fname,self.opts.output_dir) + if e.lower() == '.pdf' : # compress and make a thumbnail + thumb = '%s.%s' % (dname,self.thumbformat) + pdff = os.path.join(self.opts.output_dir,fname) + retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) + if retval == 0: + pdflist.append((fname,thumb)) + else: + pdflist.append((fname,fname)) + if (rownum+1) % 2 == 0: + fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) + else: + fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) + for logfname in logfiles: # expect at least tlog - if more + if abspath(logfname) == abspath(self.tlog): # handled later + sectionname = 'All tool run' + if (len(logfiles) > 1): + sectionname = 'Other' + ourpdfs = pdflist + else: + realname = os.path.basename(logfname) + sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log + ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname] + pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove + nacross = 1 + npdf = len(ourpdfs) + + if npdf > 0: + nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2))) + if int(nacross)**2 != npdf: + nacross += 1 + nacross = int(nacross) + width = min(400,int(1200/nacross)) + html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname) + html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>') + ntogo = nacross # counter for table row padding with empty cells + html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>') + for i,paths in enumerate(ourpdfs): + fname,thumb = paths + s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" + alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname) + if ((i+1) % nacross == 0): + s += '</tr>\n' + ntogo = 0 + if i < (npdf - 1): # more to come + s += '<tr>' + ntogo = nacross + else: + ntogo -= 1 + html.append(s) + if html[-1].strip().endswith('</tr>'): + html.append('</table></div>\n') + else: + if ntogo > 0: # pad + html.append('<td> </td>'*ntogo) + html.append('</tr></table></div>\n') + logt = open(logfname,'r').readlines() + logtext = [x for x in logt if x.strip() > ''] + html.append('<div class="toolFormTitle">%s log output</div>' % sectionname) + if len(logtext) > 1: + html.append('\n<pre>\n') + html += logtext + html.append('\n</pre>\n') + else: + html.append('%s is empty<br/>' % logfname) + if len(fhtml) > 0: + fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n') + fhtml.append('</table></div><br/>') + html.append('<div class="toolFormTitle">All output files available for downloading</div>\n') + html += fhtml # add all non-pdf files to the end of the display + else: + html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter) + html.append(galhtmlpostfix) + htmlf = file(self.opts.output_html,'w') + htmlf.write('\n'.join(html)) + htmlf.write('\n') + htmlf.close() + self.html = html + + + def run(self): + """ + scripts must be small enough not to fill the pipe! + """ + if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']: + retval = self.runBash() + else: + if self.opts.output_dir: + ste = open(self.elog,'w') + sto = open(self.tlog,'w') + sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) + sto.flush() + print("commandline is %s" % (self.cl)) + print("environment is %s" % (os.environ)) + p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir) + else: + p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE) + p.stdin.write(self.script) + p.stdin.close() + retval = p.wait() + if self.opts.output_dir: + sto.close() + ste.close() + err = open(self.elog,'r').readlines() + if retval <> 0 and err: # problem + print >> sys.stderr,err #same problem, need to capture docker stdin/stdout + if self.opts.make_HTML: + self.makeHtml() + return retval + + def runBash(self): + """ + cannot use - for bash so use self.sfile + """ + if self.opts.output_dir: + s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl) + sto = open(self.tlog,'w') + sto.write(s) + sto.flush() + p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir) + else: + p = subprocess.Popen(self.cl,shell=False) + retval = p.wait() + if self.opts.output_dir: + sto.close() + if self.opts.make_HTML: + self.makeHtml() + return retval + + +def main(): + u = """ + This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: + <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" + </command> + """ + op = argparse.ArgumentParser() + a = op.add_argument + a('--docker_image',default=None) + a('--script_path',default=None) + a('--tool_name',default=None) + a('--interpreter',default=None) + a('--output_dir',default='./') + a('--output_html',default=None) + a('--input_tab',default='None', nargs='*') + a('--output_tab',default='None') + a('--user_email',default='Unknown') + a('--bad_user',default=None) + a('--make_HTML',default=None) + a('--new_tool',default=None) + a('--dockerized',default=0) + a('--output_format', default='tabular') + a('--input_format', dest='input_formats', action='append', default=[]) + a('--additional_parameters', dest='additional_parameters', action='append', default=[]) + opts = op.parse_args() + assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user) + assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R' + if opts.output_dir: + try: + os.makedirs(opts.output_dir) + except: + pass + if opts.dockerized==0: + switch_to_docker(opts) + return + r = ScriptRunner(opts) + retcode = r.run() + os.unlink(r.sfile) + if retcode: + sys.exit(retcode) # indicate failure to job runner + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scriptrunner.xml Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,125 @@ +<tool id="docker_scriptrunner" name="Docker Scriptrunner" version="0.1.6"> + <description>Makes scripts into tools using Docker</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="0.4.0">docker-py</requirement> + </requirements> + <command> + python "$__tool_directory__/scriptrunner.py" + --script_path "$runme" + --interpreter "$interpreter" + --user_email "$__user_email__" + #if $generate_simple_output.make_TAB=="yes": + --output_tab "$tab_file" + #end if + #if $make_HTML.value=="yes": + --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" + #else: + --output_dir "." + #end if + #if $additional_parameters != 'None': + #for i in $additional_parameters: + --additional_parameters + "$i.param_name, $i.param_value" + #end for + #end if + #if $input_files != 'None': + --input_tab + #for i in $input_files: + $i.input + #end for + #for i in $input_files: + --input_format + #if str($i.in_format) == "None": + "Any" + #else + "$i.in_format" + #end if + #end for + #end if + --docker_image "$docker_image" + </command> +<configfiles> + <configfile name="runme">$dynScript</configfile> +</configfiles> + <inputs> + <repeat name="input_files" title="Select input files"> + <param name="input" type="data" label="Select an input file from your history" optional="true" size="120" + help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/> + <param name="in_format" type="select" optional="true" multiple="true" label="Optional: Select the allowed input datatype(s) for your tool/script"> + <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> + <column name="value" index="0"/> + </options> + </param> + </repeat> + <repeat name="additional_parameters" title="Set additional parameters"> + <param name="param_name" type="text" value="parameter_name" label="Choose a parameter name" size="20"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value="@_."/></valid>> + </sanitizer> + </param> + <param name="param_value" type="text" value="parameter_value" label="Enter a parameter value" size="50"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </repeat> + <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60" + help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output"> + <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option> + <option value="" selected="true">No, no HTML output file thanks</option> + </param> + <conditional name="generate_simple_output"> + <param name="make_TAB" type="select" label="Create a new history output alongside the HTML file specified above" + help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes"> + <option value="yes" selected="true">My script writes to a new history output</option> + <option value="">I do not want a new history output file</option> + </param> + <when value="yes"> + <param name="out_format" type="select" label="Select the datatype that your tool/script produces" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml"> + <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> + <column name="value" index="0"/> + </options> + </param> + </when> + <when value=""> + </when> + </conditional> + <param name="interpreter" type="select" label="Select the interpreter for your code"> + <option value="Rscript" selected="true">Rscript</option> + <option value="python">python</option> + <option value="perl">perl</option> + <option value="sh">sh</option> + </param> + <param help="The script you are pasting will be run in this image. Make sure it contains the necessary tools" label="Select a docker image" name="docker_image" type="select"> + <options from_data_table="docker_scriptrunner_images"/> + </param> + <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True" size="8x120" + help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None')."> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format_source="input" name="tab_file"> + <filter>generate_simple_output['make_TAB'] == "yes"</filter> + <actions> + <action type="format"> + <option type="from_param" name="generate_simple_output.out_format" /> + </action> + </actions> + </data> + <data format="html" name="html_file" > + <filter>make_HTML == "yes"</filter> + </data> + </outputs> +<expand macro="help_macro" /> +<expand macro="test_data_macro" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/docker_images.loc.sample Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,3 @@ +# Place here your docker images that usrs can select in the docker scriptrunner +mvdbeek/scriptrunner mvdbeek/scriptrunner +mvdbeek/scriptrunner-r-bioperl-python mvdbeek/scriptrunner-r-bioperl-python
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/docker_images.loc.sample Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,3 @@ +# Place here your docker images that usrs can select in the docker scriptrunner +mvdbeek/scriptrunner mvdbeek/scriptrunner +mvdbeek/scriptrunner-r-bioperl-python mvdbeek/scriptrunner-r-bioperl-python
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Place available docker images here --> + <table name="docker_scriptrunner_images" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/docker_images.loc.sample" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample.test Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Place available docker images here --> + <table name="docker_scriptrunner_images" comment_char="#"> + <columns>name, value</columns> + <file path="${__HERE__}/test-data/docker_images.loc.sample" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jul 08 15:09:10 2016 -0400 @@ -0,0 +1,14 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="docker-py" version="0.4.0"> + <install version="1.0"> + <actions> + <action type="setup_virtualenv">docker-py==0.4.0 + </action> + </actions> + </install> + </package> + <readme> + Only Admins can use this tool generator but please do NOT install o + </readme> +</tool_dependency>