Mercurial > repos > mmonsoor > camera_combinexsannos
changeset 20:7fab8b835557 draft
planemo upload commit a5f400649acb64e1c66a92379027ac5abdb4f546
| author | lecorguille |
|---|---|
| date | Tue, 09 Apr 2019 11:37:50 -0400 |
| parents | 608b4b95818b |
| children | ce18b7a5ef4e |
| files | README.rst abims_CAMERA_combinexsAnnos.xml lib.r macros.xml planemo_test.sh |
| diffstat | 5 files changed, 18 insertions(+), 28 deletions(-) [+] |
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--- a/README.rst Fri Feb 01 11:31:20 2019 -0500 +++ b/README.rst Tue Apr 09 11:37:50 2019 -0400 @@ -2,6 +2,10 @@ Changelog/News -------------- +**Version 2.2.5 - 09/04/2019** + +- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) + **Version 2.2.2 - 01/03/2018** - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
--- a/abims_CAMERA_combinexsAnnos.xml Fri Feb 01 11:31:20 2019 -0500 +++ b/abims_CAMERA_combinexsAnnos.xml Tue Apr 09 11:37:50 2019 -0400 @@ -209,6 +209,12 @@ Changelog/News -------------- +.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS + +**Version 2.2.5 - 09/04/2019** + +- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) + **Version 2.2.2 - 01/03/2018** - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
--- a/lib.r Fri Feb 01 11:31:20 2019 -0500 +++ b/lib.r Tue Apr 09 11:37:50 2019 -0400 @@ -36,13 +36,13 @@ #@author G. Le Corguille #The function create a zip archive from the different png generated by diffreport diffreport_png2zip <- function() { - zip("eic.zip",dir(pattern="_eic")) - zip("box.zip",dir(pattern="_box")) + zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip")) + zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip")) } #The function create a zip archive from the different tabular generated by diffreport diffreport_tabular2zip <- function() { - zip("tabular.zip",dir(pattern="tabular/*")) + zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip")) } #@author G. Le Corguille @@ -152,7 +152,7 @@ diffrep=diffrep[order(diffrep$pvalue), ] } - dir.create("tabular") + dir.create("tabular", showWarnings = FALSE) write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep="")) if (listArguments[["eicmax"]] != 0) {
--- a/macros.xml Fri Feb 01 11:31:20 2019 -0500 +++ b/macros.xml Tue Apr 09 11:37:50 2019 -0400 @@ -2,12 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.4_2">r-snow</requirement> - <requirement type="package" version="3.0.0">bioconductor-xcms</requirement> - <requirement type="package" version="1.34.0">bioconductor-camera</requirement> - <requirement type="package" version="2.28.0">bioconductor-multtest</requirement> + <requirement type="package" version="0.4_3">r-snow</requirement> + <requirement type="package" version="1.38.1">bioconductor-camera</requirement> + <requirement type="package" version="2.38.0">bioconductor-multtest</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> - <requirement type="package" version="1.3.23">graphicsmagick</requirement> + <requirement type="package" version="1.3.26">graphicsmagick</requirement> </requirements> </xml> <xml name="stdio">
--- a/planemo_test.sh Fri Feb 01 11:31:20 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -# Example of planemo command to launch test - -# Note: --galaxy_branch "dev" is set to deal with zip file - - -# -- Use of conda dependencies -planemo conda_init --conda_prefix /tmp/mc -planemo conda_install --conda_prefix /tmp/mc . -planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev" - -#All 1 test(s) executed passed. -#abims_CAMERA_combinexsAnnos[0]: passed - - -# -- Use of shed_test -planemo shed_test --install_galaxy -t testtoolshed - -#All 1 test(s) executed passed. -#testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.4[0]: passed