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Philosopher added to BioContainers#350

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osallou merged 15 commits intoBioContainers:masterfrom
ypriverol:master
Nov 29, 2019
Merged

Philosopher added to BioContainers#350
osallou merged 15 commits intoBioContainers:masterfrom
ypriverol:master

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@ypriverol
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@ypriverol ypriverol commented Nov 28, 2019

Submitting a Container

(If you're requesting for a new container, please check the procedure described here.

Check BioContainers' Dockerfile specifications

Checklist

  1. Misc
  • My tool doesn't exist in BioConda
  • The image can be built
  1. Metadata
  • LABEL base_image
  • LABEL version
  • LABEL software.version
  • LABEL about.summary
  • LABEL about.home
  • LABEL about.license
  • MAINTAINER
  1. Extra (optionals)
  • I have written tests in test-cmds.txt
  • [] LABEL extra.identifier
  • LABEL about.documentation
  • LABEL about.license_file
  • LABEL about.tags

Check BioContainers' Dockerfile metadata

ypriverol added 12 commits March 30, 2018 08:37
@ypriverol
two new cntainers from phenomenal
65e741f
@ypriverol
csifingerid added
5bf9d68
@ypriverol
bruker2batman added
d7ff337
@ypriverol
Merge branch 'master' of https://github.com/BioContainers/containers
033a3ee 
* 'master' of https://github.com/BioContainers/containers: (418 commits)
  Add debian package suitename/0.3.070628-1b1-deb/Dockerfile
  Add debian package staden/2.0.0b11-2b1-deb/Dockerfile
  Add debian package staden-io-lib-utils/1.14.8-2-deb/Dockerfile
  Add debian package staden-common/2.0.0b11-2-deb/Dockerfile
  Add debian package ssw-align/1.1-1b1-deb/Dockerfile
  Add debian package sspace/2.1.1dfsg-2-deb/Dockerfile
  Add debian package ssake/3.8.4-1-deb/Dockerfile
  Add debian package sra-toolkit/2.8.1-2dfsg-2-deb/Dockerfile
  Add debian package spread-phy/1.0.7dfsg-1-deb/Dockerfile
  Add debian package spaced/1.0.2dfsg-1b1-deb/Dockerfile
  Add debian package soapdenovo/1.05-3-deb/Dockerfile
  Add debian package smrtanalysis/020161126-deb/Dockerfile
  Add debian package smrtanalysis-dev/020161126-deb/Dockerfile
  Add debian package smithwaterman/0.020160702-1b1-deb/Dockerfile
  Add debian package sleepyhead/1.0.0-beta-2dfsg-2b1-deb/Dockerfile
  Add debian package sitplus/1.0.3-5.1-deb/Dockerfile
  Add debian package sitplus-data/1.0.3-5.1-deb/Dockerfile
  Add debian package relion-binplusmpi/1.4dfsg-2b2-deb/Dockerfile
  Add debian package relion-bin-plusmpi-plusgui/1.4dfsg-2b2-deb/Dockerfile
  Add debian package relion-bin-plusgui/1.4dfsg-2b2-deb/Dockerfile
  ...
@ypriverol
Merge branch 'master' of https://github.com/BioContainers/containers
f81bd3c 
* 'master' of https://github.com/BioContainers/containers: (375 commits)
  Testing ci scripts on jenkins
  Docker to Singularity failed in Jenkins, committing again to try once more
  Modified test-ci to check Singularity conversion
  Add a container for strelka 2.9.7 (#273)
  updated PIA to version 1.3.8
  updated PIA to version 1.3.8
  updating PIA
  Added dockerfile for new version of bedtools (2.27.0), moving from the (#267)
  seq_crumbs (#264)
  add readme (#263)
  [New Tool from BioShadock] PhyloCSF (#260)
  add interproscan container (tools only) (#258)
  add debian base image Dockerfile
  Add 10XGenomics longranger 2.2.2 (#255)
  Update Dockerfile (#254)
  [New Tool] Integron Finder (Pasteur) (#248)
  [New Tool] Peptimapper (from BioShaDock) (#251)
  Update PULL_REQUEST_TEMPLATE.md
  [New tool] mindthegap (gatb package) (#249)
  [New tool] CoreGeneBuilder 1.0 (#246)
  ...
@ypriverol
Merge branch 'master' of https://github.com/BioContainers/containers
7911740 
* 'master' of https://github.com/BioContainers/containers: (147 commits)
  update base debian image, removing unneeded stuff
  Fixed software name for new X!Tandem version.
  PIA:1.3.0: fixed authorizations on imported script
  PIA:1.3.8: fixed authorizations on imported script
  Makes run_pia.sh executable, otherwise the container fails.
  Added Dockerfile for X!Tandem 17-02-01-4
  BIODOCKER: setting old recipe up to specs
  BIOR_ANNOTATE: Fixed base image and added missing LABEL
  SPECTRA-CLUSTER-CLI:1.0-beta Fixed cmd line
  SPECTRA-CLUSTER-CLI:1.1.2 Fixed missing arg in cmd line
  PEPTIDESHAKER:1.10.3 Fixed missing variable in cmd line
  PEPTIDESHAKER:1.16.17 Fixed missing variable in cmd line
  PEPTIDESHAKER:1.16.16 Fixed missing variable in cmd line
  DENOVOGUI:1.5.2 Fix cmd line missing arg
  DENOVOGUI:1.10.4 Fix cmd line missing variable
  NOVOR_1b: Fixed cmd line missing arg
  TANDEM:15-12-15: Fixed cmd line missing arg
  TANDEM:10-12-01: Fixed cmd line missing arg
  SEARCHGUI:2.8.6: Fixed cmd line missing arg
  SEARCHGUI:2.6.0: Fixed missing argument in bin cmd line
  ...
@ypriverol
new crux version.
cb6a438
@ypriverol
Remove un-necesary files.
45a7656
@ypriverol
Crux container added.
97fef87
@ypriverol
Rollback the gitignore and gitmodules
33a52a6
@ypriverol
Merge branch 'master' of https://github.com/BioContainers/containers
0b09089 
* 'master' of https://github.com/BioContainers/containers: (859 commits)
  test for biotools integration
  add dockerfile for control-freec (#349)
  Update Dockerfile for TALON version 4.4 to create smaller container. (#347)
  Add Dockerfile for TALON version 4.4 (#346)
  Add debian package zstd/1.3.8dfsg-3-deb/Dockerfile
  Add debian package zalign/0.9.1-4-deb/Dockerfile
  Add debian package yaggo/1.5.10-2-deb/Dockerfile
  Add debian package xopen/0.5.0-2-deb-py3/Dockerfile
  Add debian package xopen/0.5.0-2-deb-py2/Dockerfile
  Add debian package xmedcon/0.16.1dfsg-1-deb/Dockerfile
  Add debian package wise/2.4.1-21-deb/Dockerfile
  Add debian package wise-data/2.4.1-21-deb/Dockerfile
  Add debian package wigeon/20101212dfsg1-2-deb/Dockerfile
  Add debian package wgerman-medical/20160103-3-deb/Dockerfile
  Add debian package vtkgdcm/2.8.8-9-deb-py3/Dockerfile
  Add debian package vtk-dicom/0.8.9-1-deb-py3/Dockerfile
  Add debian package vtk-dicom-tools/0.8.9-1-deb/Dockerfile
  Add debian package vsearch/2.10.4-1-deb/Dockerfile
  Add debian package velvetoptimiser/2.2.6-2-deb/Dockerfile
  Add debian package velvet-tests/1.2.10dfsg1-5-deb/Dockerfile
  ...
@ypriverol
Philosopher added to BioContainers
9f28aee
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biocontainers-bot commented Nov 28, 2019

No biotools label defined, please check if tool is not already defined in biotools (https://bio.tools) and add extra.identifiers.biotools label if it exists. If it is not defined, you can ignore this comment.

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biocontainers-bot commented Nov 28, 2019

No biotools label defined, please check if tool is not already defined in biotools (https://bio.tools) and add extra.identifiers.biotools label if it exists. If it is not defined, you can ignore this comment.

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biocontainers-bot commented Nov 28, 2019

No philosopher/2.0.0/test-cmds.txt (test file) present, skipping tests

osallou
osallou reviewed Nov 28, 2019
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philosopher/2.0.0/Dockerfile Outdated
RUN apt-get update && apt-get install -y wget
RUN ZIP=philosopher_linux_amd64.deb && \
wget https://github.com/Nesvilab/philosopher/releases/download/v2.0.0/$ZIP -O /tmp/$ZIP && dpkg -i /tmp/$ZIP
RUN rm -rfv /tmp/$ZIP
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@osallou osallou Nov 28, 2019

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You should put the rm on previous line, this will lower container size.

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@ypriverol ypriverol Nov 28, 2019

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I just did the changes. Please have look.

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biocontainers-bot commented Nov 28, 2019

No biotools label defined, please check if tool is not already defined in biotools (https://bio.tools) and add extra.identifiers.biotools label if it exists. If it is not defined, you can ignore this comment.

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biocontainers-bot commented Nov 28, 2019

No philosopher/2.0.0/test-cmds.txt (test file) present, skipping tests

osallou
osallou reviewed Nov 29, 2019
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philosopher/2.0.0/Dockerfile Outdated
LABEL about.tags="Proteomics"

################## MAINTAINER ######################
MAINTAINER Felipe da Veiga Leprevost <felipe@leprevost.com.br>
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@osallou osallou Nov 29, 2019

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I suppose you are the maintainer, and not felipe

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biocontainers-bot commented Nov 29, 2019

No biotools label defined, please check if tool is not already defined in biotools (https://bio.tools) and add extra.identifiers.biotools label if it exists. If it is not defined, you can ignore this comment.

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biocontainers-bot commented Nov 29, 2019

No philosopher/2.0.0/test-cmds.txt (test file) present, skipping tests

@osallou osallou merged commit b01e5a6 into BioContainers:master Nov 29, 2019
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biocontainers-bot commented Nov 29, 2019

No biotools label defined, please check if tool is not already defined in biotools (https://bio.tools) and add extra.identifiers.biotools label if it exists. If it is not defined, you can ignore this comment.

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biocontainers-bot commented Nov 29, 2019

No philosopher/2.0.0/test-cmds.txt (test file) present, skipping tests

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@ypriverol @biocontainers-bot @osallou