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jlopez
RPACIB
Commits
cab5ac5b
Commit
cab5ac5b
authored
Nov 27, 2018
by
jlopez
Browse files
Fix workflows
parent
67e65134
Changes
2
Show whitespace changes
Inline
Side-by-side
R/helper_functions.R
View file @
cab5ac5b
...
...
@@ -107,7 +107,7 @@ getInstallToolPackageWorkflow <- function(tool, containerType) {
size
<-
length
(
data
)
intalls
<-
""
res
<-
""
res
<-
c
()
for
(
tools
in
data
)
{
splitB
<-
strsplit
(
tool
,
"%"
)
...
...
@@ -118,11 +118,10 @@ getInstallToolPackageWorkflow <- function(tool, containerType) {
if
(
tools
$
version
==
version
)
{
for
(
c
in
tools
$
dependencies
)
{
tt
<-
paste0
(
c
$
name
,
"%"
,
c
$
version
)
print
(
tt
)
res
<-
paste0
(
res
,
getInstallToolPackageBioContainer
(
tt
,
containerType
))
res
<-
paste0
(
res
,
"\n"
)
res
<-
c
(
res
,
getInstallToolPackageBioContainer
(
tt
,
containerType
))
}
res
<-
paste0
(
res
,
"\t"
,
tools
$
install
,
collapse
=
'\n'
)
res
<-
c
(
res
,
paste0
(
"\t"
,
tools
$
install
,
collapse
=
'\n'
))
print
(
res
)
return
(
res
)
}
}
...
...
server/opt_home.R
View file @
cab5ac5b
...
...
@@ -517,13 +517,16 @@ createWorkflows <- function(result, haveR, haveConda) {
for
(
tool
in
selectWorkflows
){
result
<-
paste
(
result
,
'############### Install Workflow tools ##############'
,
sep
=
"\n"
)
result
<-
paste
(
result
,
'############### Install Workflow tools ##############
\n
'
,
sep
=
"\n"
)
result
<-
paste
(
result
,
getInstallToolPackageWorkflow
(
tool
,
input
$
containerType
),
sep
=
"\n\n"
)
for
(
i
in
getInstallToolPackageWorkflow
(
tool
,
input
$
containerType
))
{
result
<-
paste0
(
result
,
i
,
"\n"
)
}
}
}
else
{
select
BioTool
<-
input
$
selected
Biocontainer
select
Workflows
<-
input
$
selected
Workflows
result
<-
paste0
(
result
,
"\n"
)
...
...
@@ -573,12 +576,13 @@ createWorkflows <- function(result, haveR, haveConda) {
result
<-
paste
(
result
,
"RUN chmod 777 -R /opt/workflows/"
,
sep
=
"\n"
)
result
<-
paste
(
result
,
"ENV PATH=/opt/workflows/bin:${PATH}"
,
sep
=
"\n"
)
for
(
tool
in
selectBioTool
){
result
<-
paste
(
result
,
'############### Install Workflow ##############'
,
sep
=
"\n"
)
for
(
tool
in
selectWorkflows
){
result
<-
paste
(
result
,
'############### Install Workflow ##############\n'
,
sep
=
"\n"
)
result
<-
paste0
(
result
,
"\nRUN "
,
getInstallToolPackageWorkflow
(
tool
,
input
$
containerType
))
for
(
i
in
getInstallToolPackageWorkflow
(
tool
,
input
$
containerType
))
{
result
<-
paste0
(
result
,
"RUN"
,
i
,
"\n"
)
}
}
}
...
...
@@ -635,7 +639,7 @@ createBiocontainer <- function(result, haveR) {
for
(
tool
in
selectBioTool
){
result
<-
paste
(
result
,
'############### Install BioContainer tools ##############'
,
sep
=
"\n"
)
result
<-
paste
(
result
,
'############### Install BioContainer tools ##############
\n
'
,
sep
=
"\n"
)
result
<-
paste
(
result
,
getInstallToolPackageBioContainer
(
tool
,
input
$
containerType
),
sep
=
"\n\n"
)
...
...
@@ -684,10 +688,10 @@ createBiocontainer <- function(result, haveR) {
for
(
tool
in
selectBioTool
){
result
<-
paste
(
result
,
'############### Install BioContainer tools ##############'
,
sep
=
"\n"
)
result
<-
paste
(
result
,
'############### Install BioContainer tools ##############
\n
'
,
sep
=
"\n"
)
result
<-
paste0
(
result
,
"
\n
RUN "
,
getInstallToolPackageBioContainer
(
tool
,
input
$
containerType
))
result
<-
paste0
(
result
,
"RUN "
,
getInstallToolPackageBioContainer
(
tool
,
input
$
containerType
))
}
}
...
...
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