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HenrikBengtsson / CBI-software

A Scientific Software Stack for HPC (CentOS oriented)
https://wynton.ucsf.edu/hpc/software/software-repositories.html
5 stars 2 forks source link

hisat2: Installed files are writable by group(!) #51

Closed HenrikBengtsson closed 2 years ago

HenrikBengtsson commented 2 years ago 
ls -la /home/hb/shared/software/CBI/hisat2-2.2.0
total 92904
drwxrwxr-x   6 hb hb     4096 Feb  6  2020 .
drwxr-xr-x 124 hb hb     4096 Mar 15 21:50 ..
-rw-rw-r--   1 hb hb     1301 Jul  8  2019 AUTHORS
drwxrwxr-x   5 hb hb     4096 Feb  6  2020 example
-rwxrwxr-x   1 hb hb     5597 Jul  8  2019 extract_exons.py
-rwxrwxr-x   1 hb hb     5053 Jan 30  2020 extract_splice_sites.py
-rwxrwxr-x   1 hb hb    19634 Feb  6  2020 hisat2
-rwxrwxr-x   1 hb hb 15095992 Feb  6  2020 hisat2-align-l
-rwxrwxr-x   1 hb hb 11379296 Feb  6  2020 hisat2-align-l-debug
-rwxrwxr-x   1 hb hb 15070432 Feb  6  2020 hisat2-align-s
-rwxrwxr-x   1 hb hb 11413104 Feb  6  2020 hisat2-align-s-debug
-rwxrwxr-x   1 hb hb     2807 Jul  8  2019 hisat2-build
-rwxrwxr-x   1 hb hb  5704408 Feb  6  2020 hisat2-build-l
-rwxrwxr-x   1 hb hb  3557160 Feb  6  2020 hisat2-build-l-debug
-rwxrwxr-x   1 hb hb  5670800 Feb  6  2020 hisat2-build-s
-rwxrwxr-x   1 hb hb  3649344 Feb  6  2020 hisat2-build-s-debug
-rwxrwxr-x   1 hb hb     5597 Jul  8  2019 hisat2_extract_exons.py
-rwxrwxr-x   1 hb hb    19220 Jan 30  2020 hisat2_extract_snps_haplotypes_UCSC.py
-rwxrwxr-x   1 hb hb    34901 Feb  6  2020 hisat2_extract_snps_haplotypes_VCF.py
-rwxrwxr-x   1 hb hb     5053 Jan 30  2020 hisat2_extract_splice_sites.py
-rwxrwxr-x   1 hb hb     2689 Feb  6  2020 hisat2-inspect
-rwxrwxr-x   1 hb hb  3473056 Feb  6  2020 hisat2-inspect-l
-rwxrwxr-x   1 hb hb  1740176 Feb  6  2020 hisat2-inspect-l-debug
-rwxrwxr-x   1 hb hb  3503224 Feb  6  2020 hisat2-inspect-s
-rwxrwxr-x   1 hb hb  1760536 Feb  6  2020 hisat2-inspect-s-debug
-rwxrwxr-x   1 hb hb     4874 Feb  6  2020 hisat2_read_statistics.py
-rwxrwxr-x   1 hb hb  7059072 Feb  6  2020 hisat2-repeat
-rwxrwxr-x   1 hb hb  5314104 Feb  6  2020 hisat2-repeat-debug
-rwxrwxr-x   1 hb hb    34699 Feb  6  2020 hisat2_simulate_reads.py
-rwxrwxr-x   1 hb hb    21297 Feb  6  2020 hisatgenotype_build_genome.py
-rwxrwxr-x   1 hb hb    22690 Feb  6  2020 hisatgenotype_extract_reads.py
-rwxrwxr-x   1 hb hb    52422 Feb  6  2020 hisatgenotype_extract_vars.py
-rwxrwxr-x   1 hb hb    73747 Jul  8  2019 hisatgenotype_hla_cyp.py
-rwxrwxr-x   1 hb hb   124313 Feb  6  2020 hisatgenotype_locus.py
drwxrwxr-x   2 hb hb     4096 Feb  6  2020 hisatgenotype_modules
-rwxrwxr-x   1 hb hb    18254 Feb  6  2020 hisatgenotype.py
drwxrwxr-x   2 hb hb     4096 Feb  6  2020 hisatgenotype_scripts
-rw-rw-r--   1 hb hb    35147 Jul  8  2019 LICENSE
-rw-rw-r--   1 hb hb    65305 Jan 30  2020 MANUAL
-rw-rw-r--   1 hb hb    79265 Jul  8  2019 MANUAL.markdown
-rw-rw-r--   1 hb hb      584 Jul  8  2019 NEWS
drwxrwxr-x   2 hb hb     4096 Feb  6  2020 scripts
-rw-rw-r--   1 hb hb      202 Jan 30  2020 TUTORIAL
-rw-rw-r--   1 hb hb        6 Feb  6  2020 VERSION
HenrikBengtsson commented 2 years ago

This was fixed by #47