changeset 1:ecd0a79e8130 draft

planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docker/Dockerfile	Fri May 03 11:01:43 2019 -0400
@@ -0,0 +1,36 @@
+# Galaxy - PIPE_T
+#
+# VERSION       0.2
+
+FROM bgruening/galaxy-stable:latest
+
+MAINTAINER D. CANGELOSI, [e-mail]
+
+ENV GALAXY_CONFIG_BRAND="Galaxy PIPE-T"
+ENV ENABLE_TTS_INSTALL True
+ 
+RUN apt-get -y update
+RUN apt-get install -y libxml2-dev libcurl4-openssl-dev curl libcairo2-dev
+
+#Workaround for ubuntu
+#RUN cp /etc/ssl/private/ssl-cert-snakeoil.key /etc/
+#RUN chown root:ssl-cert /etc/ssl-cert-snakeoil.key
+#RUN sed -i -e "s/\/ssl\/private//g" /etc/postgresql/9.3/main/postgresql.conf
+
+#install pipe_t from toolshed
+ADD tools.yml $GALAXY_ROOT/tools.yaml
+RUN install-tools $GALAXY_ROOT/tools.yaml && \
+    /tool_deps/_conda/bin/conda clean --all --yes
+
+#RUN chown galaxy:galaxy /usr/local/lib/R/site-library
+
+# Mark folders as imported from the host.
+#VOLUME ["/export/", "/data/", "/var/lib/docker"]
+
+# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy)
+EXPOSE :80
+EXPOSE :21
+EXPOSE :8800
+
+# Autostart script that is invoked during container start
+CMD ["/usr/bin/startup"]

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docker/tools.yml	Fri May 03 11:01:43 2019 -0400
@@ -0,0 +1,46 @@
+# This is a sample file to be used as a reference for populating a list of
+# tools that you wish to install into Galaxy from a Tool Shed via the
+# `install_tool_shed_tools.py` script.
+#
+# For each tool you want to install, you must provide the following keys:
+#  * name: this is is the name of the tool to install
+#  * owner: owner of the Tool Shed repository from where the tools is being
+#           installed
+# Further, you need to provide **one** of the following two keys:
+#  * tool_panel_section_id: ID of the tool panel section where you want the
+#                           tool to be installed. The section ID can be found
+#                           in Galaxy's `shed_tool_conf.xml` config file. Note
+#                           that the specified section must exist in this file.
+#                           Otherwise, the tool will be installed outside any
+#                           section.
+#  * tool_panel_section_label: Display label of a tool panel section where
+#                              you want the tool to be installed. If it does not
+#                              exist, this section will be created on the target
+#                              Galaxy instance (note that this is different than
+#                              when using the ID).
+#                              Multi-word labels need to be placed in quotes.
+#                              Each label will have a corresponding ID created;
+#                              the ID will be an all lowercase version of the
+#                              label, with multiple words joined with
+#                              underscores (e.g., 'BED tools' -> 'bed_tools').
+#
+# Tou can also specify the following optional keys to further define the
+# installation properties:
+#  * tool_shed_url: the URL of the Tool Shed from where the tool should be
+#                   insta: True
+#  * revisions: a list of revisions of the tool, all of which will attempt to
+#               be installed. (default: latest)
+#  * install_tool_dependencies: True or False - whether to install tool
+#                               dependencies or not. (default: True)
+#  * install_repository_dependencies: True or False - whether to install repo
+#                               dependencies or not. (default: True)
+
+api_key: admin
+galaxy_instance: http://localhost:8080
+
+tools:
+- name: pipe_t
+  owner: davidecangelosi
+  tool_panel_section_label: "PIPE-T"
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+  install_tool_dependencies: True

--- a/pipe-t.xml	Thu May 02 04:49:04 2019 -0400
+++ b/pipe-t.xml	Fri May 03 11:01:43 2019 -0400
@@ -9,7 +9,7 @@
   <requirement type="package" version="1.56.0">bioconductor-impute</requirement>
 <requirement type="package" version="1.11.0">r-bbmisc</requirement>
 <requirement type="package" version="1.8.4">r-psych</requirement>
-<requirement type="package" version="1.8_1">r-zoo</requirement>
+<requirement type="package" version="1.8_3">r-zoo</requirement>
 <requirement type="package" version="2.10.0">bioconductor-nondetects</requirement>
 <requirement type="package" version="4.1_1">r-hmisc</requirement>
 </requirements>