安裝官網(wǎng)https://regtools.readthedocs.io/en/latest/#installation

git clone https://github.com/griffithlab/regtools
cd regtools/
mkdir build
cd build/
cmake ..
make

vim ~/.bashrc
export PATH=/data1/jiarongf/specise_compare_HGPS/AS/regtools/build:$PATH
source ~/.bashrc
ls
regtools
regtools --help

(leafcutter) 17:10:04 jiarongf@222.197.214.27:/data1/jiarongf/specise_compare_HGPS/AS/regtools/build
$
regtools --help

Program:        regtools
Version:        0.0.1
Usage:          regtools <command> [options]
Command:        junctions               Tools that operate on feature junctions (e.g. exon-exon junctions from RNA-seq).
                cis-ase                 Tools related to allele specific expression in cis.
                cis-splice-effects      Tools related to splicing effects of variants.
                variants                Tools that operate on variants.

接著安裝 leafcutter

安裝方法http://davidaknowles.github.io/leafcutter/articles/Installation.html

git clone https://github.com/davidaknowles/leafcutter

install.packages("rstan")

報錯了

install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
Installing package into ‘/home/jiarongf/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository https://mc-stan.org/r-packages/src/contrib:
  cannot open URL 'https://mc-stan.org/r-packages/src/contrib/PACKAGES'
trying URL 'https://cloud.r-project.org/src/contrib/rstan_2.21.7.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://cloud.r-project.org/src/contrib/rstan_2.21.7.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://cloud.r-project.org/src/contrib/rstan_2.21.7.tar.gz': status was 'Peer certificate cannot be authenticated with given CA certificates'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘rstan’ failed

去試試手動安裝吧
還是手動安裝比較實在亿昏，直接去這個鏈接下載，然后tools安裝就好了，

安裝成功

install leafcutter

devtools::install_github("davidaknowles/leafcutter/leafcutter")

報錯

ERROR: dependencies ‘doMC’, ‘intervals’, ‘DirichletMultinomial’, ‘TailRank’ are not available for package ‘leafcutter’

install.packages('doMC')
Installing package into ‘/home/jiarongf/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/doMC_1.3.8.tar.gz'
Content type 'application/x-gzip' length 154488 bytes (150 KB)
==================================================
downloaded 150 KB

* installing *source* package ‘doMC’ ...
** package ‘doMC’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (doMC)

The downloaded source packages are in
        ‘/data1/tmp/RtmpRTagaG/downloaded_packages’


install.packages('intervals')
install.packages('DirichletMultinomial')
Installing package into ‘/home/jiarongf/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
Warning message:
package ‘DirichletMultinomial’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

BiocManager::install('DirichletMultinomial')
BiocManager::install('TailRank')

安裝依賴包結(jié)束示惊，都可以library成功
再去安裝leafcutter

devtools::install_github("davidaknowles/leafcutter/leafcutter")
library(leafcutter)
Loading required package: Rcpp

安裝成功！