Hello Sandy 👋

I will show the steps to run Deciphon server and populate it with some data so that you can better test deciphon_web.

Assuming you have Docker installed, you can enter

docker compose --env-file compose.cfg up

to start it. Check out http://127.0.0.1:8000/docs for the API documentation.

You probably won't need any custom configuration. But if you think you do, check out compose.cfg for information.

You can use deciphonctl to populate it with protein database and to perform scans.

You can install it via

pipx install deciphonctl

(Or via pip if you prefer it.)

You will need to direct deciphonctl to the server:

export DECIPHONCTL_SCHED_URL=http://127.0.0.1:8000
export DECIPHONCTL_S3_URL=http://127.0.0.1:9000/deciphon

And now we can add a protein database and scan a sequence against it:

# Upload minifam.hmm for processing according to NCBI genetic code 11
deciphonctl hmm add minifam.hmm 11

# Check its processing state
deciphonctl hmm ls

# Once it is done, you should be able
# to see the protein database by entering
deciphonctl db ls

# Submit a sequence for scan against
# minifam database
deciphonctl scan add enzime.fna 1

# Check its state
deciphonctl scan ls

# Once it is done, visualize its result
deciphonctl scan snap-view 1

The last output should be similar to:

Alignments for each domain:
== domain 1  score: 247.9 bits;  conditional E-value: 2.9e-78
               HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTTT--GGGSEE--STTS-HH CS
PF00742.20   3 ISTLKESLIGDRITRIEGILNGTMNYILTEMEEEGASFSEALKEAQQLGYAEADPTDDVEGLDAARKLAILARLAFGLEVELEDVEVEAIEKLTAE 98
               istlkesl gdritriegilngt+nyiltemeeegasfsealkeaq+lGyaEaDptdDveGlDaarKlailarlafgleveledveve iekltae
             1 ISTLKESLIGDRITRIEGILNGTMNYILTEMEEEGASFSEALKEAQQLGYAEADPTDDVEGLDAARKLAILARLAFGLEVELEDVEVEAIEKLTAE 96
    enzime   1 ATACAGTCAGGCAACAGGATAGCTATACAGAGGGGGTTTGGCAGGCCTGTGGGGCAGGGGGCGGGAACGACGATGTGTGGGTGGGGGGGAGACAGG 284
               TCCTAACTTGAGTCGTAGTTAGCGAATTCATAAAGCCTCACTAACAATGACACACCAATAGTACCGATCTTCGTCTGTATATAATATACTAATCCA
               TGGCGGGGATCTTTACAGAACC..TCTCTGGGAGGTACTGGGGGAGAGCCGAGTTGCTGAGATTTAGGATACAGATGAGCGGGCAGGAATAGGTCA
               ................................................................................................
               ................................................................................................
               79********************************************************************************************** PP

               HHHHHHCTTEEEEEEEEECEEEEEEEEEETTSGGGHSSST.EEEEEEESSSEE..EEEEES-SSHHHHHHHH CS
PF00742.20  99 DIEKIKEEGKVLKLVASAVEARVKPELVPKSHPLASVKGSDNAVAVETERHSVgeLVVQGPGAGEEPTASAV 170
               die+ keegkvlklvasavearvkpelvpkshplasvkgsdnavaveter++   lvvqGpgaG+epTAsav
            97 DIEKIKEEGKVLKLVASAVEARVKPELVPKSHPLASVKGSDNAVAVETERHSVGELVVQGPGAGEEPTASAV 168
    enzime 287 GAGAAAGGGAGTACGGAGGGGAGACGCGCATCCTGTGAGTGAGGGGGAGCCTGGGCGGCGCGGGGGCAGTGG 501
               ATAATAAAGATTATTCGCTACGTACATTCACACTCCTAGCAACTCTACAGACGGATTTAGCGCGAACCCCCT
               TTAAAGAGTATAAAGACCCACGCGTGGATGATAACGAACTCCCGTAAGAATTTCACAGGAAGTCAGACACTA
               ....................................................A...................
               ........................................................................
               *************************************************987667***************** PP