Update documentation reflect recent changes with riboWaltz

XPRESSyourself · Apr 5, 2020 · d143a9f · d143a9f
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diff --git a/README.md b/README.md
@@ -13,17 +13,6 @@
 -----
 Please refer to the [documentation](https://xpresspipe.readthedocs.io/en/latest/?badge=latest) for more in depth details.
 
-### Announcement:
-Currently, R is struggling to auto-install riboWaltz for p-site QC. If you run into issues in the time-being, please open an R session in your environment and run the following commands:
-```
-install.packages("devtools", repos = "http://cran.us.r-project.org")
-devtools::install_github("LabTranslationalArchitectomics/riboWaltz", dependencies = c("Depends", "Imports", "LinkingTo"))
-
-# And then run the following to test installation:
-library(riboWaltz)
-```
-
-
 ### Citation:    
 ```
 Berg JA, et. al. (2020). XPRESSyourself: Enhancing, standardizing, and

diff --git a/docs/content/beginner.rst b/docs/content/beginner.rst
@@ -49,7 +49,7 @@ Generate Reference Files
   ### Change these ###
   $ echo 'GTF_URL=ftp://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz' >> fetch.sh
   $ echo 'FASTA_URL=ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome' >> fetch.sh
-  $ echo 'CHROMOSOMES="1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y"'
+  $ echo 'CHROMOSOMES="1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y"' >> fetch.sh
   ####################
 
   $ echo 'curl -O $GTF_URL' >> fetch.sh
@@ -183,14 +183,7 @@ Install
   $ conda activate xpresspipe
   $ pip install ./XPRESSpipe
 
-| 4. If using XPRESSpipe for ribosome profiling data, we recommend manually installing riboWaltz as its auto-installation is not stable in the XPRESSpipe script since the software is not available through a package manager like Bioconductor or Conda. You can do this by opening an interactive R session in your :data:`xpresspipe` conda environment.
-
-.. code-block:: shell
-
-  $ conda activate xpresspipe
-  $ R
-
-| 5. Let's test this to make sure everything is operating properly:
+| 4. Let's test this to make sure everything is operating properly:
 
 .. code-block:: shell
 

diff --git a/docs/content/installation.rst b/docs/content/installation.rst
@@ -49,31 +49,13 @@ Install XPRESSpipe
 
 .. code-block:: shell
 
-  $ python setup.py install
+  $ pip install .
   $ xpresspipe test
 
 | - If a summary menu appeared in the command line interface, it means we are good to go! Congrats! You are almost ready to use XPRESSpipe!
 | - You can run :data:`xpresspipe --help` to see a list of the available modules within XPRESSpipe. To see specific parameters for a module, type :data:`xpresspipe <module_name> --help`.
 
 
-------------------------------
-Important!
-------------------------------
-| Currently, R is struggling to auto-install riboWaltz for p-site QC. If you run into issues in the time-being, please open an R session in your environment and run the following commands:
-
-.. code-block:: R
-
-  install.packages("devtools", repos = "http://cran.us.r-project.org")
-
-  devtools::install_github("LabTranslationalArchitectomics/riboWaltz", dependencies = c("Depends", "Imports", "LinkingTo"))
-
-| And then run the following to test installation:
-
-.. code-block:: R
-
-  library(riboWaltz)
-
-
 ==============================================================
 Using XPRESSpipe in a supercomputing environment (i.e. SLURM)
 ==============================================================