Mercurial > repos > mingchen0919 > aurora_skewer

annotate skewer_render.R @ 9:c0e57c994deb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
author mingchen0919
date Thu, 26 Apr 2018 14:10:58 -0400
parents c5c297020c36
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
1 ##============ Sink warnings and errors to a file ==============
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
2 ## use the sink() function to wrap all code within it.
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
3 ##==============================================================
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
4 zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt'))
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
5 sink(zz)
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
6 sink(zz, type = 'message')
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
7
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
8 #============== preparation ====================================
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
9 options(stringsAsFactors = FALSE)
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
10 # import libraries
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
11 #------------------------------------------------------------------
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
12 # ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
13 #------------------------------------------------------------------
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
14 library('getopt')
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
15 library('rmarkdown')
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
16 library('htmltools')
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
17
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
18
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
19 # load helper functions
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
20 source(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/helper.R'))
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
21 # import getopt specification matrix from a csv file
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
22 opt = getopt(getopt_specification_matrix('getopt_specification.csv',
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
23 tool_dir=Sys.getenv('TOOL_INSTALL_DIR')))
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
24 # define environment variables for all input values. this is useful when we
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
25 # want to use input values by other programming language in r markdown
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
26 do.call(Sys.setenv, opt[-1])
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
27 #===============================================================
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
28
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
29
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
30 #======================== render Rmd files =========================
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
31 # NOTICE:
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
32 # we should copy all rmarkdown files from tool install directory to REPORT_FILES_PATH directory.
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
33 # and render rmarkdown files in the REPORT_FILES_PATH directory.
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
34 file.copy(from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
35 to = Sys.getenv('REPORT_FILES_PATH'), recursive = TRUE)
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
36 system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
37
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
38 #----------------BELOW IS WHERE YOU NEED TO CUSTOMIZE ---------------------
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
39 render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/skewer.Rmd'))
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
40 # add more lines below if there are more Rmd files to be rendered
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
41
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
42 #===============================================================
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
43
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
44
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
45 #============== expose outputs to galaxy history ===============
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
46 system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs.sh')
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
47 #===============================================================
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
48
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
49
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
50 ##--------end of code rendering .Rmd templates----------------
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
51 sink()
c5c297020c36 planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents:
diff changeset
52 ##=========== End of sinking output=============================