From d143a9f2acfd758afa44a04698c7c08b950d2439 Mon Sep 17 00:00:00 2001 From: j-berg Date: Sat, 4 Apr 2020 21:59:04 -0600 Subject: [PATCH] Update documentation reflect recent changes with riboWaltz --- README.md | 11 ----------- docs/content/beginner.rst | 11 ++--------- docs/content/installation.rst | 20 +------------------- 3 files changed, 3 insertions(+), 39 deletions(-) diff --git a/README.md b/README.md index af143c1..b6dc8b1 100644 --- 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 index e92ad77..ebe58e7 100644 --- 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 index f38e865..b2209c8 100644 --- 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 --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) ==============================================================