Mercurial > repos > saskia-hiltemann > ireport
changeset 2:e8755431a0cd draft
fixed missing dependencies
| author | saskia-hiltemann |
|---|---|
| date | Tue, 30 Sep 2014 09:47:14 -0400 |
| parents | 440f4aa3db97 |
| children | 4a6ebda2a3ae |
| files | README.md iReport.sh iReport.xml tool_dependencies.xml |
| diffstat | 4 files changed, 38 insertions(+), 4 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Sep 30 09:47:14 2014 -0400 @@ -0,0 +1,24 @@ +iReport +======= + +iReport Galaxy tool - HTML reporting in Galaxy + +install to your Galaxy via the main tool shed: http://toolshed.g2.bx.psu.edu/ + +direct repository link: http://saskia-hiltemann@toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/ireport + +email: s.hiltemann@erasmusmc.nl + + + + +Planned changes +--------------- +- ~~option to download iReport webpage~~ +- more pluggable code to add content item types etc. +- markdown instead of plain text/html in text fields. +- multiple columns in table converted to weblinks. +- table colums link to archive files in history +- .. +- ..suggestions anyone? +
--- a/iReport.sh Wed Jul 30 07:03:43 2014 -0400 +++ b/iReport.sh Tue Sep 30 09:47:14 2014 -0400 @@ -1,5 +1,5 @@ #!/bin/bash -repositorypath="/mnt/galaxyTools/shed_tools/toolshed.nbic.nl/repos/saskia-hiltemann/ireport/71dc132e9bb2/ireport" # TODO: dependency +#repositorypath="/mnt/galaxyTools/shed_tools/toolshed.nbic.nl/repos/saskia-hiltemann/ireport/71dc132e9bb2/ireport" # TODO: dependency source "${repositorypath}/createHTML.sh" echo "allparams: $@" @@ -15,8 +15,8 @@ while [ $# -gt 0 ] do case "$1" in - --toolpath) repositorypath=$2;shift;; - --galaxypath) galaxypath=$2;shift;; + --toolpath) repositorypath=$2;shift;; + --galaxypath) galaxypath=$2;shift;; --minwidth) minwidth=$2;shift;; --tab) tabs+=",$2";shift;; --item) items+=",$2";shift;;
--- a/iReport.xml Wed Jul 30 07:03:43 2014 -0400 +++ b/iReport.xml Tue Sep 30 09:47:14 2014 -0400 @@ -1,10 +1,13 @@ <tool id="iReport" name="iReport" version="1"> <description> create an HTML report </description> - + <requirements> + <requirement type="set_environment">REPOSITORY_PATH</requirement> + </requirements> <command interpreter="bash"> iReport.sh + --toolpath \$REPOSITORY_PATH --galaxypath ${report.files_path} --htmlout ${report} --minwidth ${minwidth}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Sep 30 09:47:14 2014 -0400 @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="REPOSITORY_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> +</tool_dependency> +