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Amine GHOZLANE
shaman
Commits
a52f364c
Commit
a52f364c
authored
Aug 29, 2019
by
Amine GHOZLANE
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Add conda install
parent
c1430724
Pipeline
#14057
failed
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4 changed files
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140 additions
and
14 deletions
+140
-14
.gitlab-ci.yml
.gitlab-ci.yml
+15
-11
conda_inst/build.sh
conda_inst/build.sh
+8
-0
conda_inst/meta.yaml
conda_inst/meta.yaml
+115
-0
ui.R
ui.R
+2
-3
No files found.
.gitlab-ci.yml
View file @
a52f364c
...
...
@@ -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
conda_inst/build.sh
0 → 100644
View file @
a52f364c
#!/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
conda_inst/meta.yaml
0 → 100644
View file @
a52f364c
{
%
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
ui.R
View file @
a52f364c
...
...
@@ -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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