Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

mf,json,jx files annotated #32

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

mf,json,jx files annotated #32

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
236 changes: 189 additions & 47 deletions blast/blast.json
View file
Open in desktop

Large diffs are not rendered by default.

16 changes: 13 additions & 3 deletions blast/blast.jx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
],
"outputs": [format("small.fasta.%d", x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT))],
"local_job": true,
"category": "preprocessing"
},
{
"command": format(
Expand All @@ -41,14 +42,21 @@
"outputs": [
format("small.fasta.%d.out", x),
format("small.fasta.%d.err", x),
]
],
"resources" : {
"cores":1,
"memory":1000,
"disk":1400,
"wall-time":40
},
"category": "simulation"
} for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)),
{
"command": format(
"%s output.fasta %s",
CAT_BLAST,
join([format("small.fasta.%d.out", x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT))]),
),
),
"inputs": [
CAT_BLAST,
format("small.fasta.%d.out", x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)),
Expand All @@ -57,19 +65,21 @@
"output.fasta"
],
"local_job": true,
"category": "analysis",
},
{
"command": format(
"cat %s > output.fasta.err",
join([format("small.fasta.%d.err", x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT))]),
),
),
"inputs": [
format("small.fasta.%d.err", x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)),
],
"output": [
"output.fasta.err"
],
"local_job": true,
"category": "analysis"
},
],
}
10 changes: 9 additions & 1 deletion blast/blast.mf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,14 @@

CATEGORY=preprocessing

small.fasta.0 small.fasta.1 small.fasta.2 small.fasta.3 small.fasta.4 small.fasta.5 small.fasta.6 small.fasta.7 small.fasta.8 small.fasta.9 small.fasta.10 small.fasta.11 small.fasta.12 small.fasta.13 small.fasta.14 small.fasta.15 small.fasta.16 small.fasta.17 small.fasta.18 small.fasta.19 : small.fasta split_fasta
LOCAL ./split_fasta 10 small.fasta

CATEGORY=simulation
CORES=1
MEMORY=1000
DISK=1400
WALLTIME=40

small.fasta.0.out small.fasta.0.err : blastall small.fasta.0 nt
./blastall -p blastn -d nt/nt -i small.fasta.0 -o small.fasta.0.out 2> small.fasta.0.err

Expand Down Expand Up @@ -63,6 +69,8 @@ small.fasta.18.out small.fasta.18.err : blastall small.fasta.18 nt
small.fasta.19.out small.fasta.19.err : blastall small.fasta.19 nt
./blastall -p blastn -d nt/nt -i small.fasta.19 -o small.fasta.19.out 2> small.fasta.19.err

CATEGORY=analysis

output.fasta : cat_blast small.fasta.0.out small.fasta.1.out small.fasta.2.out small.fasta.3.out small.fasta.4.out small.fasta.5.out small.fasta.6.out small.fasta.7.out small.fasta.8.out small.fasta.9.out small.fasta.10.out small.fasta.11.out small.fasta.12.out small.fasta.13.out small.fasta.14.out small.fasta.15.out small.fasta.16.out small.fasta.17.out small.fasta.18.out small.fasta.19.out
LOCAL ./cat_blast output.fasta small.fasta.0.out small.fasta.1.out small.fasta.2.out small.fasta.3.out small.fasta.4.out small.fasta.5.out small.fasta.6.out small.fasta.7.out small.fasta.8.out small.fasta.9.out small.fasta.10.out small.fasta.11.out small.fasta.12.out small.fasta.13.out small.fasta.14.out small.fasta.15.out small.fasta.16.out small.fasta.17.out small.fasta.18.out small.fasta.19.out

Expand Down
Loading