From 39e07579e5965410444c571085952af5735dd657 Mon Sep 17 00:00:00 2001 From: JIANHONG OU Date: Mon, 19 Feb 2024 08:47:28 -0500 Subject: [PATCH] fix multiple 2023 to 2024. --- Dockerfile | 2 +- vignettes/scripts.Rmd | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index 9c96fe4..08d53d1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -88,7 +88,7 @@ RUN cd ~ && git clone https://github.com/pachterlab/sleuth && \ RUN git clone https://github.com/kundajelab/phantompeakqualtools && \ Rscript -e "install.packages('phantompeakqualtools/spp_1.14.tar.gz')" -RUN path="/usr/local/lib/R/site-library/basicBioinformaticsDRC2023/extdata" && \ +RUN path="/usr/local/lib/R/site-library/basicBioinformaticsDRC2024/extdata" && \ rm -rf ~/sleuth && \ cp -r $path/RNAseq /home/rstudio/ && \ cp -r $path/ChIPseq /home/rstudio/ diff --git a/vignettes/scripts.Rmd b/vignettes/scripts.Rmd index faa9e0b..5de855d 100644 --- a/vignettes/scripts.Rmd +++ b/vignettes/scripts.Rmd @@ -59,13 +59,13 @@ All the following steps are running in Rstudio "Terminal" or "Console". You may want to open the source of "scripts.Rmd" at the "Source Panes" by ```{r, eval=FALSE} -rstudioapi::documentOpen("/usr/local/lib/R/site-library/basicBioinformaticsDRC2023/doc/scripts.Rmd") +rstudioapi::documentOpen("/usr/local/lib/R/site-library/basicBioinformaticsDRC2024/doc/scripts.Rmd") ``` ## Run kallisto and Salmon for RNA-seq The sample files are packaged -in basicBioinformaticsDRC2023 package and Docker container. +in basicBioinformaticsDRC2024 package and Docker container. Now we will download the zebrafish cDNA files from ENSEMBL in order to build the Kallisto and Salmon transcript index. If you are doing rRNA depletion library, @@ -92,7 +92,7 @@ chromosome 4, 13, 16 and 21 to speed up the test run. mkdir data/RNAseq cd data/RNAseq # wget https://raw.githubusercontent.com/jianhong/genomictools/master/inst/extdata/Danio_rerio.GRCz11.cdna.toy.fa.gz -ln -s /usr/local/lib/R/site-library/basicBioinformaticsDRC2023/extdata/Danio_rerio.GRCz11.cdna.toy.fa.gz ./ +ln -s /usr/local/lib/R/site-library/basicBioinformaticsDRC2024/extdata/Danio_rerio.GRCz11.cdna.toy.fa.gz ./ ``` It will take several seconds to build the toy index. @@ -177,7 +177,7 @@ If you have trouble in downloading the data from ensembl, try to load the pre-sa object for the toy data. ```{r, eval=FALSE} # t2g <- readRDS(url("https://raw.githubusercontent.com/jianhong/genomictools/master/inst/extdata/t2g.rds")) -t2g <- readRDS(system.file("extdata", "t2g.rds", package = "basicBioinformaticsDRC2023")) +t2g <- readRDS(system.file("extdata", "t2g.rds", package = "basicBioinformaticsDRC2024")) head(t2g, n=3) ``` @@ -281,7 +281,7 @@ The data are only a subset of the whole genome. We will only use genes in chromosome 4, 13, 16 and 21 to speed up the test run. ```{bash, eval=FALSE} # wget https://raw.githubusercontent.com/jianhong/genomictools/master/inst/extdata/Danio_rerio.GRCz11.dna.toy.fa.gz -ln -s /usr/local/lib/R/site-library/basicBioinformaticsDRC2023/extdata/Danio_rerio.GRCz11.dna.toy.fa.gz ./ +ln -s /usr/local/lib/R/site-library/basicBioinformaticsDRC2024/extdata/Danio_rerio.GRCz11.dna.toy.fa.gz ./ ## the following step will take about 3min bwa index -p GRCz11.toy Danio_rerio.GRCz11.dna.toy.fa.gz ```