Linux-shell 脚本

(base) Mar402 20:35:03 ~
$ which Rscript
/usr/bin/Rscript
(base) Mar402 20:35:23 ~
$ conda activate R4
(R4) Mar402 20:35:44 ~ #在不同的环境下 Rscript不一样
$ which Rscript
/trainee/Mar402/miniconda3/envs/R4/bin/Rscript
(R4) Mar402 20:39:33 ~
$ conda activate RNA
(RNA) Mar402 20:39:49 ~
$ echo $PATH | tr ':' '\n'
/trainee/Mar402/bin
~/bin
/trainee/Mar402/miniconda3/envs/RNA/bin
/trainee/Mar402/miniconda3/condabin
/usr/local/sbin
/usr/local/bin
/usr/sbin
/usr/bin
/sbin
/bin
/usr/games
/usr/local/games
/snap/bin #不同环境中调用不同的内容，是因为conda已经将PATH改了

(R4) Mar402 21:01:29 ~
$ vim file1.sh #条件1 存在这个文件
(R4) Mar402 21:05:26 ~
$ bash file1.sh
hi!
(R4) Mar402 21:05:39 ~
$ ll -thr file1.sh
-rw-rw-r-- 1 Mar402 Mar402 31 Apr  4 21:05 file1.sh
(R4) Mar402 21:06:35 ~
$ chmod u+x file1.sh #条件二 添加权限
(R4) Mar402 21:06:42 ~
$ ll -thr file1.sh
-rwxrw-r-- 1 Mar402 Mar402 31 Apr  4 21:05 file1.sh*
(R4) Mar402 21:06:51 ~
$ mv file1.sh* bin/ #条件三移到PATH可以搜到的范围
(R4) Mar402 21:07:34 ~
$ ls bin
ace2sam                                 hisatgenotype_build_genome.py
AUTHORS                                 hisatgenotype_extract_reads.py
blast2sam.pl                            hisatgenotype_extract_vars.py
bowtie2sam.pl                           hisatgenotype_hla_cyp.py
doc                                     hisatgenotype_locus.py
example                                 hisatgenotype_modules
export2sam.pl                           hisatgenotype.py
extract_exons.py                        hisatgenotype_scripts
extract_splice_sites.py                 interpolate_sam.pl
fasta-sanitize.pl                       LICENSE
file1.sh                                MANUAL
hisat2                                  MANUAL.markdown
hisat2-2.1.0                            maq2sam-long
hisat2-align-l                          maq2sam-short
hisat2-align-l-debug                    md5fa
hisat2-align-s                          md5sum-lite
hisat2-align-s-debug                    NEWS
hisat2-build                            novo2sam.pl
hisat2-build-l                          plot-ampliconstats
hisat2-build-l-debug                    plot-bamstats
hisat2-build-s                          psl2sam.pl
hisat2-build-s-debug                    sam2vcf.pl
hisat2_extract_exons.py                 samtools
hisat2_extract_snps_haplotypes_UCSC.py  samtools.pl
hisat2_extract_snps_haplotypes_VCF.py   scripts
hisat2_extract_splice_sites.py          seq_cache_populate.pl
hisat2-inspect                          soap2sam.pl
hisat2-inspect-l                        TUTORIAL
hisat2-inspect-l-debug                  VERSION
hisat2-inspect-s                        wgsim
hisat2-inspect-s-debug                  wgsim_eval.pl
hisat2_simulate_reads.py                zoom2sam.pl
(R4) Mar402 21:07:40 ~
$ file1.sh #直接可被当命令执行
hi!

(R4) Mar402 21:15:54 ~
$ bash ~/bin/file1.sh 1>test.log 2>&1