update instructions

docs/index.md

@@ -2,9 +2,7 @@
 
 Welcome to our Platform guidelines web-page. Here analysts and developers will find guidelines on how to work with our most common environments.
 
-We are developing platforms for each analysis type we have experience with at HCBC. Currently we fully support:
-
-- bulk RNAseq analysis ![](https://img.shields.io/badge/status-beta-blue)
+We are developing platforms for each analysis type we have experience with at HCBC.
 
 Go to each analysis-type section to learn how to use our platform.
 
@@ -14,54 +12,96 @@ Go to each analysis-type section to learn how to use our platform.
     * Remove `bcbio` from you `PATH` by commenting the line in your `.bashrc` if you have it
     * Start Rstudio with these modules on: `gcc/9.2.0 imageMagick/7.1.0 geos/3.10.2 cmake/3.22.2 R/4.3.1 fftw/3.3.10 gdal/3.1.4 udunits/2.2.28  boost/1.75.0`
     * Add `--exclude=compute-f-17-[09-25]` to the 'Slurm Custom Arguments' field
-    * When the session is started, set you library path typing this command in your console Rstudio window:  `.libPaths("/n/app/bcbio/R4.3.1_rnaseq")`
+    * When the session is started, set you library path typing this command in your console Rstudio window:  `.libPaths("/n/app/bcbio/R4.3.1")`
 
 * Load bcbioR with `library(bcbioR)`
-* Make sure the version is 0.3.0 with this command `packageVersion("bcbioR")` or re-install with `devtools::install_github("bcbio/bcbioR",build_manual = TRUE, build_vignettes = TRUE)`, if you are in your own environment
+* Make sure the version is **v0.3.*** with this command `packageVersion("bcbioR")` or re-install with `devtools::install_github("bcbio/bcbioR",build_manual = TRUE, build_vignettes = TRUE)`, if you are in your own environment
 
 ## General Project
 
 Use the [hcbc app](https://hcbc.connect.hms.harvard.edu/content/8cd62872-0ec9-4905-8920-c745d2375758) to set up projects names. This name will be used for O2/FAS/github and dropbox. They may be already defined in the Trello card.
 
 This set up needs [bcbioR](https://github.com/bcbio/bcbioR) and [usethis](https://usethis.r-lib.org) packages.
 
-Make sure the version is `0.3.0` with this command `packageVersion("bcbioR")` or re-install with `devtools::install_github("bcbio/bcbioR",build_manual = TRUE, build_vignettes = TRUE)`, if you are in your own environment
-
-* Create an R Project located in your project folder: `usethis::proj_activate("/path/to/analysis/folder")`
-* Deploy folders/files compatible with any project: `bcbioR::bcbio_templates(type="base", outpath="/path/to/analysis/folder")`
-* Start a git repository: `usethis::use_git()`
-
-If you want to push this project to GitHub, follow these steps:
+Make sure the version is `v0.3.*` with this command `packageVersion("bcbioR")` or re-install with `devtools::install_github("bcbio/bcbioR",build_manual = TRUE, build_vignettes = TRUE)`, if you are in your own environment.
+
+First create Rstudio project:
+
+```
+project_path <- "/n/scratch/groups/hsph/hbc/lp113/lastname_postdoc_rnaseq_human_heart_hbc00000"
+# if path doesn't exists - normally not the case
+dir.create(project_path)
+usethis::proj_activate(project_path)
+```
+
+This will restart the session in the project directory:
+
+```
+# Make sure is v0.3*
+packageVersion("bcbioR")
+# check current library
+.libPaths()
+# set up needed library
+.libPaths("/n/app/bcbio/R4.3.1_rnaseq")
+# check package version again
+packageVersion("bcbioR")
+# Set this library for future use - only once
+bcbioR::use_library("/n/app/bcbio/R4.3.1_rnaseq")
+# Deploy base project
+bcbioR::bcbio_templates(type="base", outpath=".", org="hcbc")
+# Start local git repository
+# Don't commit files and restart session
+usethis::use_git()
+```
+
+Push this project to GitHub following these steps:
 
 * Only once every 30 days, set up your github credentials: `usethis::gh_token_help()`
   * **NOTE** You may want to run this first to keep this token working in future sessions in O2/FAS: `git config --global credential.helper store`
 * Push repository to HBC github as private: `usethis::use_github(org="hbc",private=TRUE)`
 
+Read the REAME and any other Management checklist that is in the project folder.
+
 ## RNAseq
 
-Use this common library path to perform your analysis: `.libPaths("/n/app/bcbio/R4.3.1_rnaseq")`.
-* Follow the previous step to set up the [base](#general-project) project
-* Follow this instruction https://bcbio.github.io/bcbioR/#set-rnaseq-report-folder to start your **RNAseq** analysis
+Use this common library path to perform your analysis: `bcbio::use_library("/n/app/bcbio/R4.3.1_rnaseq")`.
+* Follow the previous step to set up the [base](#general-project) project if you haven't done it already
+* Deploy templates with:
+
+```
+bcbioR::bcbio_templates(type="rnaseq", outpath="reports")
+```
 
 ## scRNAseq
 
-Please, change to this common library path to perform your analysis: `.libPaths("/n/app/bcbio/R4.3.1_singlecell")`.
+Please, change to this common library path to perform your analysis: 
+
+```
+bcbio::use_library("/n/app/bcbio/R4.3.1_singlecell")
+bcbioR::bcbio_templates(type="singlecell, outpath="reports")
+```
 
 ## ChipSeq
 
-Please, change to this common library path to perform your analysis: `.libPaths("/n/app/bcbio/R4.3.1_chipseq")`.
+Please, change to this common library path to perform your analysis: 
+
+```
+bcbio::use_library("/n/app/bcbio/R4.3.1_chipseq")
+bcbioR::bcbio_templates(type="chipseq, outpath="reports")
+```
 
 # bcbioR supported templates
 
 We used `bcbioR` to deploy folders and code to our project directories to improve robustness in our analysis.
 
 You can install `bcbioR` as indicated here: `https://github.com/bcbio/bcbioR/tree/main`
 
-- RNAseq ![](https://img.shields.io/badge/status-alpha-blue)
-- CELLCHAT ![](https://img.shields.io/badge/status-alpha-yellow)
-TEASeq ![](https://img.shields.io/badge/status-concept-yellow)
-- COSMX ![](https://img.shields.io/badge/status-concept-yellow)
-- scRNAseq ![](https://img.shields.io/badge/status-concept-yellow)
+- RNAseq ![](https://img.shields.io/badge/status-stable-blue)
+- ChipSeq ![](https://img.shields.io/badge/status-beta-yellow)
+- scRNAseq ![](https://img.shields.io/badge/status-beta-yellow)
+- CELLCHAT ![](https://img.shields.io/badge/status-draft-grey)
+- TEASeq ![](https://img.shields.io/badge/status-draft-grey)
+- COSMX ![](https://img.shields.io/badge/status-draft-grey)
 
 
 # Note