search

vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
Other
278 stars 54 forks source link

Can I use the Macbook to do the DiaNN? #428

Open lzy604 opened 2 years ago

lzy604 commented 2 years ago

Dear authors,

It is really a nice software. I want to use my MacBook to do the analysis in terminal. Is there any codes for this? Thanks

vdemichev commented 2 years ago

No, unfortunately does not work on Mac

lzy604 commented 2 years ago

Is there any methods to install this software on the sever to perform the analysis? I mean not by using the interface one, just use the command in terminal/

vdemichev commented 2 years ago

Yes, the Linux version.

njohnso6 commented 2 years ago

Unfortunately, it is difficult to install on a server using an rpm package since as users we don't have installation permissions. Is there any way other than with Visual Studio to build it in order to just use the command line as a standalone program, without the GUI? I don't see any other makefiles.

vdemichev commented 2 years ago

All the installer (both Windows and Linux) does is unpack the files in a particular folder, can also do this manually.

helloimbavani commented 1 year ago

Hi,

Is it possible to run DIA-NN on a virtual computer? I tried exactly that, but all i got was the following:

diann.exe --f "C:\Proteomics\Lysate_BG\230424_BG_OE_C20_pooled_5.raw " --f "C:\Proteomics\Lysate_BG\230424_BG_OE_HMC3_pooled_7.raw " --lib "C:\Proteomics\Lysate_BG\Output_FragPipe\library.tsv" --threads 4 --verbose 1 --out "C:\Proteomics\Lysate_BG\Output_diaNN\report.tsv" --qvalue 0.01 --matrices --out-lib "C:\Proteomics\Lysate_BG\Output_diaNN\report-lib.tsv" --gen-spec-lib --predictor --reannotate --fasta "C:\Proteomics\uniprot-download_true_format_fasta_query__28_28proteome_3AUP00000564-2023.06.07-05.44.51.46.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K,R --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal

DIA-NN exited DIA-NN-plotter.exe "C:\Proteomics\Lysate_BG\Output_diaNN\report.stats.tsv" "C:\Proteomics\Lysate_BG\Output_diaNN\report.tsv" "C:\Proteomics\Lysate_BG\Output_diaNN\report.pdf" PDF report will be generated in the background

Any thoughts, help or suggestions would be appreciated.

vdemichev commented 1 year ago

What do you see if you launch diann.exe from the command line? Was it installed in a regular way using the installer?

helloimbavani commented 1 year ago

Yes, I did install it the normal way. I just downloaded it off github (https://github.com/vdemichev/DiaNN/releases/tag/1.8.1)