2022-11-08_AS实践1 leafcutter-安装2-regtools install

安装官网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 [email protected]:/data1/jiarongf/specise_compare_HGPS/AS/regtools/build
$
regtools --help

Program:        regtools
Version:        0.0.1
Usage:          regtools  [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.

接着安装 leafcutter

安装方法http://davidaknowles.github.io/leafcutter/articles/Installation.html

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

install.packages("rstan")

报错了

这个目录根本找不到，所以dev安装不上Using devtools (recommended)
那就剩下最后两种安装方式

我的conda有问题
所以
看看这里

有没有什么解决方法

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

去试试手动安装吧
还是手动安装比较实在，直接去这个链接下载，然后tools安装就好了，

安装成功

install leafcutter

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

报错

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')

安装依赖包结束，都可以library成功
再去安装leafcutter

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

安装成功！