Commit a52f364c authored by Amine  GHOZLANE's avatar Amine GHOZLANE

Add conda install

parent c1430724
Pipeline #14057 failed
......@@ -36,14 +36,18 @@ build_master:
- master
# build_conda:
# image: continuumio/miniconda3:latest
# stage: build_conda
# before_script:
# - conda config --add channels bioconda
# - conda config --add channels conda-forge
# - conda config --add channels aghozlane
# - conda config --set anaconda_upload yes
# script:
# - anaconda login --username "$DOCKER_USER" --password "$DOCKER_PASS"
# - conda-build conda_inst
\ No newline at end of file
build_conda:
image: continuumio/miniconda3:latest
stage: build_conda
before_script:
- conda config --add channels bioconda
- conda config --add channels conda-forge
- conda config --add channels r
- conda config --add channels aghozlane
- conda config --set anaconda_upload yes
- conda install conda-verify
- conda install anaconda-client
script:
- anaconda login --username "$DOCKER_USER" --password "$DOCKER_PASS"
- conda-build conda_inst
\ No newline at end of file
#!/bin/bash
BINDIR="$PREFIX/bin"
#mkdir $BINDIR
cp -R $SRC_DIR/shamanapp $BINDIR
cp -R $SRC_DIR/KronaRShy $BINDIR
cp -R $SRC_DIR/shaman_bioblend $BINDIR
cp $BINDIR/shamanapp/www/shaman_conda.R $BINDIR/
chmod +x $BINDIR/shaman_conda.R
{% set version = GIT_DESCRIBE_TAG %}
package:
name: shaman
version: {{ version }}
channels:
- defaults
- conda-forge
- bioconda
- r
- aghozlane
source:
- git_url: https://gitlab.pasteur.fr/aghozlan/shaman.git
git_rev: {{ version }}
folder: shamanapp
- git_url: https://github.com/aghozlane/KronaRShy.git
git_rev: 0.9
folder: KronaRShy
- git_url: https://github.com/aghozlane/shaman_bioblend.git
git_rev: 1.0
folder: shaman_bioblend
requirements:
host:
- r-base
- python=3
- libgfortran=3.0.0
run:
- libgfortran=3.0.0
- r-base
- python=3
- r-rcpp
- r-shiny
- r-rjson
- r-ape
- r-psych
- r-ggplot2
- r-vegan
- r-dendextend
- r-circlize
#- bioconductor-genefilter
#- bioconductor-summarizedexperiment
- r-biocmanager
- r-googlevis
- r-shinyjs
- r-dt
- r-rcolorbrewer
- r-gplots
- r-ade4
- r-scales
- r-phytools
- r-shinywidgets
- r-sendmailr
- r-shinybs
- r-flexdashboard
- r-backports
- r-readr
- r-jsonlite
- r-shinyfiles
- r-htmltools
- r-colourpicker
- r-data.table
- r-upsetr
- r-ggrepel
- r-igraph
- r-visnetwork
- r-philentropy
- r-ramcharts
- r-gunifrac
- r-scatterd3
- r-d3heatmap
- r-biomformatshaman
- r-rnvd3shaman
- r-kronar
- r-phylotreemetar
- r-treeweightd3
- r-deseq2shaman
- r-d3vennr
- r-devtools
- r-shinytoastr
- r-shinydashboardshaman
- lockfile
- python-daemon
- bioblend
test:
commands:
- 'R -e "libshaman=c(\"shiny\", \"rjson\", \"ape\", \"GUniFrac\", \"psych\", \"ggplot2\", \"vegan\", \"dendextend\",
\"circlize\", \"genefilter\", \"SummarizedExperiment\", \"shinyjs\", \"DT\", \"RColorBrewer\",
\"gplots\", \"ade4\", \"scales\", \"phytools\", \"philentropy\", \"shinyWidgets\", \"sendmailR\",
\"shinyBS\", \"tools\", \"flexdashboard\", \"backports\", \"readr\", \"jsonlite\", \"shinyFiles\",
\"htmltools\", \"rAmCharts\", \"colourpicker\", \"data.table\", \"UpSetR\", \"ggrepel\", \"igraph\",
\"visNetwork\", \"shinytoastr\", \"scatterD3\", \"devtools\", \"shinydashboardshaman\", \"d3heatmap\",
\"biomformatshaman\", \"rNVD3shaman\", \"DESeq2shaman\", \"PhyloTreeMetaR\", \"treeWeightD3\", \"d3vennR\",
\"googleVis\"); lapply(libshaman, require, character.only = TRUE)"'
imports:
- daemon
- lockfile
- bioblend
about:
home: http://shaman.pasteur.fr
license: GPL (>= 3)
summary: 'SHAMAN is a SHiny application for Metagenomic ANalysis including a bioinformatic workflow, the statistical analysis and multiple visualization.'
description: |
SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment
of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, …).
The statistical analysis performed by SHAMAN is based on DESeq2 R package Anders and Huber 2010 ] which robustly identifies the differential abundant
features as suggested in McMurdie and Holmes 2014 and Jonsson2016. SHAMAN robustly identifies the differential abundant genera with the Generalized
Linear Model implemented in DESeq2 Love 2014. SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and generated
figures can be downloaded in several formats. Hereafter is the global workflow of the SHAMAN application:
dev_url: https://github.com/aghozlane/shaman
license_family: GPL3
......@@ -254,9 +254,8 @@ function(request) {
p("Conda installation of SHAMAN is available on linux and soon on mac. It can be performed as follow: ",style = "font-family: 'times'; font-si16pt"),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',
"# Download and install SHAMAN", br(),
"conda create -n shaman -c aghozlane shaman", br(),
"conda activate shaman", br(),
"# Now run shaman", br(), "Rscript shaman"), width=6,class="mainwell"))
"conda install -c aghozlane shaman", br(),
"# Now run shaman", br(), "Rscript shaman_conda.R"), width=6,class="mainwell"))
)
)
)
......
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