Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
ensembl-gh-mirror
ensembl
Commits
b5456a24
Commit
b5456a24
authored
Jun 05, 2009
by
Ian Longden
Browse files
nofarm option fixed
parent
3a1b84c7
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
37 additions
and
1 deletion
+37
-1
misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
...scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
+33
-1
misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
+4
-0
No files found.
misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
View file @
b5456a24
...
...
@@ -126,9 +126,41 @@ sub submit_exonerate {
my
$output
=
$self
->
get_class_name
()
.
"
_
"
.
$ensembl_type
.
"
_1.map
";
my
$cmd
=
<<EON;
$exonerate_path $query $target --showvulgar false --showalignment FALSE --ryo "xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n" $options_str | grep '^xref' > $root_dir/$output
EON
print
"
none farm command is
$cmd
\n
"
if
(
$mapper
->
verbose
);
# write details of job to database
my
$sth
=
$mapper
->
xref
->
dbc
->
prepare
("
insert into process_status (status, date) values('mapping_submitted',now())
");
$sth
->
execute
();
$sth
->
finish
;
my
$jobid
=
1
;
if
(
$ensembl_type
eq
"
peptide
"){
$jobid
=
2
;
}
for
(
my
$i
=
1
;
$i
<=
1
;
$i
++
){
my
$command
=
"
$exonerate_path
$query
$target
--showvulgar false --showalignment FALSE --ryo
"
.
'
"xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n"
'
.
"
$options_str
| grep
"
.
'
"
'
.
"
^xref
"
.
'
"
'
.
"
>
$root_dir
/
$output
";
my
$insert
=
"
insert into mapping (job_id, type, command_line, percent_query_cutoff, percent_target_cutoff, method, array_size) values(
$jobid
, '
$ensembl_type
', '
$command
',
"
.
$self
->
query_identity_threshold
.
"
,
"
.
$self
->
target_identity_threshold
.
"
, '
"
.
$self
->
get_class_name
()
.
"
',
$i
)
";
$sth
=
$mapper
->
xref
->
dbc
->
prepare
(
$insert
);
$sth
->
execute
;
$sth
->
finish
;
$sth
=
$mapper
->
xref
->
dbc
->
prepare
("
insert into mapping_jobs (root_dir, map_file, status, out_file, err_file, array_number, job_id) values (?,?,?,?,?,?,?)
");
my
$map_file
=
$self
->
get_class_name
()
.
"
_
"
.
$ensembl_type
.
"
_
"
.
$i
.
"
.map
";
my
$out_file
=
"
xref_0_
"
.
$ensembl_type
.
"
.
"
.
$jobid
.
"
-
"
.
$i
.
"
.out
";
my
$err_file
=
"
xref_0_
"
.
$ensembl_type
.
"
.
"
.
$jobid
.
"
-
"
.
$i
.
"
.err
";
$sth
->
execute
(
$root_dir
,
$map_file
,
'
SUBMITTED
',
$out_file
,
$err_file
,
$i
,
$jobid
);
}
$sth
->
finish
;
system
(
$cmd
);
$self
->
jobcount
(
1
);
return
"
nofarm
";
...
...
misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
View file @
b5456a24
...
...
@@ -38,6 +38,7 @@ sub new {
$self
->
xref
(
$mapper
->
xref
);
$self
->
mapper
(
$mapper
);
$self
->
verbose
(
$mapper
->
verbose
);
$self
->
nofarm
(
$mapper
->
nofarm
);
return
$self
;
}
...
...
@@ -528,6 +529,9 @@ sub submit_depend_job {
if
(
defined
(
$self
->
nofarm
)){
my
$sth
=
$self
->
xref
->
dbc
->
prepare
("
insert into process_status (status, date) values('mapping_finished',now())
");
$sth
->
execute
();
$sth
->
finish
;
return
;
}
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment