--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue Nov 24 18:55:08 2020 +0000
@@ -0,0 +1,115 @@
+INTRODUCTION
+============
+
+This tool is part of the xcms/camera/XSeeker workflow, and it inserts
+between camera and XSeeker. It takes in input a rdata producd by camera,
+gather some data from mzxml original files, and create a database
+containing all these informations organized in such a way that XSeeker
+has just to display the data without manipulating them anymore, which
+makes it a lot faster and easier to use.
+
+
+PREREQUISITES
+=============
+There is not real preriquesite to understand how this tool works
+and to modify it. There is a single R script - XSeekerPreparator.R - that do
+all the work.
+
+You can make this tool work alone, but you can integrate it with galaxy.
+In this case, you need to have a galaxy instance you can configure.
+It is also recomended to have access to the datatypes definitions (in
+the python files) to make the outputs recognized by galaxy as XSeeker's
+database files.
+
+
+DESIGN
+======
+This tool is very simple and does a little number of things, so there is
+only a single file: XSeekerPreparator.R .
+There is a test/test.sh file that can be used as an example to know how
+to use this tool.
+
+You will find the galaxy patches in the galaxy/ directory. These files
+are not meant to be copy/paste-ed. The content of these files must be
+added to the existing files of your galaxy instance
+
+
+REQUIREMENT
+=====
+
+ - R-4.0.0
+ - optparse
+ - xcms
+ - blob
+ - fst
+ - DBModelR
+ - stringr
+ - optparse
+ - galaxy (optional)
+
+#### R 4.0.0
+ - `export R_MAJOR=4 R_VERSION=4.0.0 BUILD_TARGET_DIR=~/R/`
+ - `wget https://cran.rstudio.com/src/base/R-${R_MAJOR}/R-${R_VERSION}.tar.gz`
+ - `tar -xf "R-${R_VERSION}.tar.gz"`
+ - `cd ./R-${R_VERSION}/`
+ - `./configure --prefix="${BUILD_TARGET_DIR}" --with-readline="no" --with-x="no"`
+ - `export CC="gcc -fPIC"`
+ - `make`
+ - `make install`
+
+#### Packages
+```bash
+~/R/bin/R -e "
+install.packages(
+    c(
+        'optparse',
+        'blob',
+        'fst',
+        'stringr',
+        'optparse',
+        'RSQLite',
+        'remotes',
+        'BiocManager'
+    ), repos='https://cloud.r-project.org'
+)" && \
+~/R/bin/R -e '
+    remotes::install_github("LainPavot/DBModelR", force=TRUE)
+' && \
+~/R/bin/R -e '
+    BiocManager::install("xcms")
+'
+```
+
+#### galaxy
+```bash
+git clone https://github.com/galaxyproject/galaxy
+```
+
+DEPLOY
+=====
+
+Install the tool in galaxy:  
+Open each file in the galaxy/ directory and copy their content to their
+respective files in your galaxy instance.  
+Copy XSeekerPreparator.R in galaxy/tool/tools/LC-MSMS/
+
+METADATA
+--------
+
+ - **@name**: XSeekerPreparator
+ - **@version**: 1.1.2
+ - **@authors**: Lain Pavot
+ - **@date creation**: 15/09/2020
+
+NOTES
+-----
+Developed and tested using:
+
+ - R 4.0.0
+ - optparse 1.6.6
+ - xcms 3.10.2
+ - blob 1.2.1
+ - fst 0.9.4
+ - DBModelR
+ - stringr 1.4.0
+ - galaxy 21.01
\ No newline at end of file