TRUST4 installation via Github repo - Issue

[RViuj]

Hi,

I am sorry for reaching out to you again. However, since I wasn't able to figure out "libbam" issue, I removed/uninstalled everything that I tried until now and this time tried to create a PAT token to install TRUST4 using the Github repo as mentioned firstly in the "install" section. However, this time, when I used the command below in the terminal;

"brew tap liulab-dfci/homebrew-trust4 && brew install trust4"

It returned:

==> Tapping liulab-dfci/trust4
Cloning into '/opt/homebrew/Library/Taps/liulab-dfci/homebrew-trust4'...
Username for 'https://github.com': RViuj
Password for 'https://[email protected]': [I copy pasted the PAT token]

and it returned:

remote: Repository not found.
fatal: repository 'https://github.com/liulab-dfci/homebrew-trust4/' not found
Error: Failure while executing; git clone https://github.com/liulab-dfci/homebrew-trust4 /opt/homebrew/Library/Taps/liulab-dfci/homebrew-trust4 --origin=origin --template= --config core.fsmonitor=false exited with 128.

May I know if I am making a mistake in defining the repository path or Homebrew path or anything else to fix this?

Thank you.

[mourisl]

I never tried to "brew install" TRUST4. The brew is to install the appropriate gcc if the system-default one does not work. You shall just run

git clone https://github.com/liulab-dfci/TRUST4.git
cd TRUST4
make

to compile TRUST4. Then you can run "path_trust4"/run-trust4 to execute the program.

[RViuj]

I previously tried the three steps you suggested and then used "./trust4 -f ~/TRUST4/ref/hg38_bcrtcr.fa -b D001_BAM.bam -o /Users/RV/Desktop/BAM/D001_BAM_TRUST4 --clonotype --igh --tcr", to execute TRUST4. However, it just returned TRUST4 OPTIONS/help menu.

[mourisl]

Probably this is due to that "--clonotype", "--igh", "--tcr" is not part of TRUST4 options. Furthermore, the hg38_bcrtcr.fa is not in the ref subfolder.

[RViuj]

Oh, my bad. I should have excluded clonotype, igh and tcr. Thank you. So, do the outputs include: trust_raw.out, trust_final.out trust_annot.fa trust_cdr3.out reports trust_report.tsv

Regarding "hg38_bcrtcr.fa", I found it in the TRUST4 folder. Screenshot attached. If it is not "hg38_bcrtcr.fa" for "-f String" may I know what could it be ? Thank you and I am really sorry for taking your time. Your suggestion will be very help.