Merge pull request #8 from galaxyproteomics/17.05

update to 17.05

.travis.yml

@@ -13,22 +13,17 @@ git:
   submodules: false
 
 before_install:
-  - export GALAXY_TRAVIS_USER=galaxy
-  - export GALAXY_UID=1450
-  - export GALAXY_GID=1450
-  - export GALAXY_HOME=/home/galaxy
-  - export [email protected]
-  - export [email protected]
-  - export GALAXY_USER_PASSWD=admin
-  - export BIOBLEND_GALAXY_API_KEY=admin
-  - export BIOBLEND_GALAXY_URL=http://localhost:8080
+  - wget https://raw.githubusercontent.com/bgruening/galaxy-flavor-testing/master/Makefile
+  - make docker_install
+  - travis_wait 75 make docker_build
+  - make docker_run
+  - sleep 300
 
-  - sudo apt-get update -qq
-  - sudo apt-get install docker-engine --no-install-recommends -y -o Dpkg::Options::="--force-confmiss" -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew"
-
-  - docker --version
-  - docker info
+install:
+  - make install
 
 script:
-  - travis_wait 45 docker build -t galaxy-docker/test .
-
+  - make test_api
+  - make test_ftp
+  - make test_bioblend
+  #- make test_docker_in_docker

Dockerfile

@@ -1,26 +1,13 @@
 # Galaxy - GalaxyP
-#
-# VERSION       0.1
 
-FROM quay.io/bgruening/galaxy:17.01
+FROM bgruening/galaxy-sequence-tools:17.05
 
 MAINTAINER Björn A. Grüning, [email protected]
 
 ENV GALAXY_CONFIG_BRAND Galaxy for Proteomic Research
 
 # Install tools
 ADD galaxyp.yaml $GALAXY_ROOT/tools.yaml
-ADD galaxyp_wf.yaml $GALAXY_ROOT/workflows.yaml
 
-RUN install-tools $GALAXY_ROOT/workflows.yaml && \
-    install-tools $GALAXY_ROOT/tools.yaml
-
-# Data libraries
-ADD library_data.yaml $GALAXY_ROOT/library_data.yaml
-
-# Download training data and populate the data library
-RUN startup_lite && \
-    sleep 60 && \
-    . $GALAXY_VIRTUAL_ENV/bin/activate && \
-    python /usr/local/lib/python2.7/dist-packages/ephemeris/setup_data_libraries.py -i $GALAXY_ROOT/library_data.yaml && \
-    workflow-install --workflow_path $GALAXY_HOME/workflows/ -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD
+RUN install-tools $GALAXY_ROOT/tools.yaml && \
+    /tool_deps/_conda/bin/conda clean --tarballs

galaxyp.yaml

@@ -41,54 +41,6 @@ galaxy_instance: http://localhost:8080
 install_resolver_dependencies: true
 install_tool_dependencies: false
 tools:
-- name: fasta_compute_length
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: fasta_merge_files_and_filter_unique_sequences
-  owner: galaxyp
-  tool_panel_section_label: "FASTA Tools"
-
-- name: seq_filter_by_id
-  owner: peterjc
-  tool_panel_section_label: "FASTA Tools"
-
-- name: seq_rename
-  owner: peterjc
-  tool_panel_section_label: "FASTA Tools"
-
-- name: seq_select_by_id
-  owner: peterjc
-  tool_panel_section_label: "FASTA Tools"
-
-- name: fasta_formatter
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: fasta_nucleotide_changer
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: fasta_to_tabular
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: find_subsequences
-  owner: bgruening
-  tool_panel_section_label: "FASTA Tools"
-
-- name: tabular_to_fasta
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: fasta_filter_by_length
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: decoyfasta
-  owner: galaxyp
-  tool_panel_section_label: "FASTA Tools"
-
 - name: text_processing
   owner: bgruening
   tool_panel_section_id: "textutil"
@@ -97,14 +49,6 @@ tools:
   owner: devteam
   tool_panel_section_id: "textutil"
 
-- name: regex_find_replace
-  owner: jjohnson
-  tool_panel_section_id: "textutil"
-
-- name: bedtools
-  owner: iuc
-  tool_panel_section_label: "BED Tools"
-
 - name: translate_bed_sequences
   owner: jjohnson
   tool_panel_section_label: "BED Tools"
@@ -129,36 +73,10 @@ tools:
   owner: galaxyp
   tool_panel_section_label: "BLAST"
 
-- name: blast_plus_remote_blastp
-  owner: galaxyp
-  tool_panel_section_label: "BLAST"
-
 - name: mgf_formatter
   owner: galaxyp
   tool_panel_section_id: convert
 
-- name: morpheus
-  owner: galaxyp
-  tool_panel_section_label: "Post Translational Modifications"
-
-- name: package_directag
-  owner: galaxyp
-
-- name: package_myrimatch
-  owner: galaxyp
-
-- name: package_mgf_formatter
-  owner: galaxyp
-
-- name: package_ltq_iquant_cli
-  owner: galaxyp
-
-- name: package_idpqonvert
-  owner: galaxyp
-
-- name: package_tagrecon
-  owner: galaxyp
-
 - name: directag_and_tagrecon
   owner: galaxyp
   tool_panel_section_label: Bumbershoot
@@ -183,14 +101,6 @@ tools:
   owner: galaxyp
   tool_panel_section_id: utils
 
-- name: ms_wiff_loader
-  owner: galaxyp
-  tool_panel_section_id: utils
-
-- name: myrimatch
-  owner: galaxyp
-  tool_panel_section_label: Bumbershoot
-
 - name: peptide_to_gff
   owner: galaxyp
   tool_panel_section_id: utils
@@ -199,10 +109,6 @@ tools:
   owner: galaxyp
   tool_panel_section_id: utils
 
-- name: proteinpilot
-  owner: galaxyp
-  tool_panel_section_id: utils
-
 - name: protxml_to_xls
   owner: galaxyp
   tool_panel_section_id: utils
@@ -211,28 +117,6 @@ tools:
   owner: galaxyp
   tool_panel_section_id: utils
 
-- name: openms
-  owner: galaxyp
-  tool_panel_section_label: OpenMS
-
-- name: spectrast
-  owner: iracooke
-  tool_panel_section_label: SpectraST
-
-- name: feature_alignment
-  owner: galaxyp
-  tool_panel_section_label: SpectraST
-
-- name: spectrast2spectrast_irt
-  owner: galaxyp
-  tool_panel_section_label: SpectraST
-  tool_shed_url: http://testtoolshed.g2.bx.psu.edu/
-
-- name: spectrast2tsv
-  owner: galaxyp
-  tool_panel_section_label: SpectraST
-  tool_shed_url: http://testtoolshed.g2.bx.psu.edu/
-
 - name: percolator
   owner: galaxyp
   tool_panel_section_label: Percolator