data-raw/build_gencode_human.R
In LieberInstitute/GenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode
library("sgejobs")
library("sessioninfo")
unlink("build_gencode_human.sh")
job_loop(
loops = list(genome = c("hg19", "hg38")),
name = "build_gencode_human",
task_num = 1,
create_shell = TRUE,
queue = "bluejay",
email = "a"
)
## Update the number of tasks to match the version numbers
array_submit("build_gencode_human.sh", task_ids = "23-32", submit = FALSE, restore = FALSE)
# ## Write the script to run
# cat(
# "## Build genomic state objects for multiple Gencode versions
#
# library('GenomicState')
# library('AnnotationDbi')
# library('sessioninfo')
#
# dir.create('gencode', showWarnings = FALSE)
# version <- Sys.getenv('SGE_TASK_ID')
#
# ## Build and save the TxDb object
# gencode_v\\${SGE_TASK_ID}_${genome}_txdb <- gencode_txdb(\\${SGE_TASK_ID}, '${genome}')
#
# ## Workaround for an RSQLite::sqliteCopyDatabase() error
# saveDb(gencode_v\\${SGE_TASK_ID}_${genome}_txdb, file = '~/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite')
# system('mv ~/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite gencode/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite')
#
# ## Build and save the annotateTranscripts output
# gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes<- gencode_annotated_genes(gencode_v\\${SGE_TASK_ID}_${genome}_txdb)
# save(gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes, file = 'gencode/gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes.rda')
#
# ## Build and save the GenomicState
# gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState <- gencode_genomic_state(gencode_v\\${SGE_TASK_ID}_${genome}_txdb)
# save(gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState, file = 'gencode/gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState.rda')
#
# ## Reproducibility information
# print('Reproducibility information:')
# Sys.time()
# proc.time()
# options(width = 120)
# session_info()
# ",
# file = 'build_gencode_human_run.R'
# )
## Update the script to run
script <- readLines("build_gencode_human.sh")
script[grepl("Rscript", script)] <- "Rscript -e \"library('GenomicState'); library('AnnotationDbi'); library('sessioninfo'); dir.create('gencode', showWarnings = FALSE); gencode_v\\${SGE_TASK_ID}_${genome}_txdb <- gencode_txdb('\\${SGE_TASK_ID}', '${genome}'); saveDb(gencode_v\\${SGE_TASK_ID}_${genome}_txdb, file = '~/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite'); system('mv ~/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite gencode/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite'); gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes<- gencode_annotated_genes(gencode_v\\${SGE_TASK_ID}_${genome}_txdb); save(gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes, file = 'gencode/gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes.rda'); gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState <- gencode_genomic_state(gencode_v\\${SGE_TASK_ID}_${genome}_txdb); save(gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState, file = 'gencode/gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState.rda'); print('Reproducibility information:'); Sys.time(); proc.time(); options(width = 120); session_info()\""
writeLines(script, "build_gencode_human.sh")
## Now run with: sh build_gencode_human.sh
system("sh build_gencode_human.sh")
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 3.6.1 Patched (2019-09-06 r77160)
# os CentOS Linux 7 (Core)
# system x86_64, linux-gnu
# ui X11
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz US/Eastern
# date 2019-10-03
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date lib source
# assertthat 0.2.1 2019-03-21 [2] CRAN (R 3.6.1)
# backports 1.1.4 2019-04-10 [2] CRAN (R 3.6.1)
# cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
# codetools 0.2-16 2018-12-24 [3] CRAN (R 3.6.1)
# colorout * 1.2-2 2019-09-26 [1] Github (jalvesaq/colorout@641ed38)
# colorspace 1.4-1 2019-03-18 [2] CRAN (R 3.6.1)
# crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
# digest 0.6.21 2019-09-20 [1] CRAN (R 3.6.1)
# dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.1)
# ggplot2 3.2.1 2019-08-10 [1] CRAN (R 3.6.1)
# glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
# gtable 0.3.0 2019-03-25 [2] CRAN (R 3.6.1)
# hms 0.5.1 2019-08-23 [2] CRAN (R 3.6.1)
# htmltools 0.3.6 2017-04-28 [2] CRAN (R 3.6.1)
# htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.6.1)
# httpuv 1.5.2 2019-09-11 [1] CRAN (R 3.6.1)
# jsonlite 1.6 2018-12-07 [2] CRAN (R 3.6.1)
# later 0.8.0 2019-02-11 [2] CRAN (R 3.6.1)
# lattice 0.20-38 2018-11-04 [3] CRAN (R 3.6.1)
# lazyeval 0.2.2 2019-03-15 [2] CRAN (R 3.6.1)
# lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.1)
# lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.6.1)
# magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
# munsell 0.5.0 2018-06-12 [2] CRAN (R 3.6.1)
# pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.1)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
# png 0.1-7 2013-12-03 [2] CRAN (R 3.6.1)
# promises 1.0.1 2018-04-13 [2] CRAN (R 3.6.1)
# pryr 0.1.4 2018-02-18 [2] CRAN (R 3.6.1)
# purrr 0.3.2 2019-03-15 [2] CRAN (R 3.6.1)
# R6 2.4.0 2019-02-14 [2] CRAN (R 3.6.1)
# Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.1)
# readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
# rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.1)
# rmote * 0.3.4 2019-09-26 [1] Github (cloudyr/rmote@fbce611)
# scales 1.0.0 2018-08-09 [2] CRAN (R 3.6.1)
# servr 0.15 2019-08-07 [1] CRAN (R 3.6.1)
# sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
# sgejobs * 0.99.0 2019-09-26 [1] Github (LieberInstitute/sgejobs@94a6151)
# stringi 1.4.3 2019-03-12 [2] CRAN (R 3.6.1)
# stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
# tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.1)
# tidyr 1.0.0 2019-09-11 [1] CRAN (R 3.6.1)
# tidyselect 0.2.5 2018-10-11 [2] CRAN (R 3.6.1)
# vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.1)
# withr 2.1.2 2018-03-15 [2] CRAN (R 3.6.1)
# xfun 0.10 2019-10-01 [1] CRAN (R 3.6.1)
# zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.1)
#
# [1] /users/lcollado/R/3.6
# [2] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-3.6/R/3.6/lib64/R/site-library
# [3] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-3.6/R/3.6/lib64/R/library
LieberInstitute/GenomicState documentation built on May 12, 2023, 5:15 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library("sgejobs")
library("sessioninfo")
unlink("build_gencode_human.sh")
job_loop(
loops = list(genome = c("hg19", "hg38")),
name = "build_gencode_human",
task_num = 1,
create_shell = TRUE,
queue = "bluejay",
email = "a"
)
## Update the number of tasks to match the version numbers
array_submit("build_gencode_human.sh", task_ids = "23-32", submit = FALSE, restore = FALSE)
# ## Write the script to run
# cat(
# "## Build genomic state objects for multiple Gencode versions
#
# library('GenomicState')
# library('AnnotationDbi')
# library('sessioninfo')
#
# dir.create('gencode', showWarnings = FALSE)
# version <- Sys.getenv('SGE_TASK_ID')
#
# ## Build and save the TxDb object
# gencode_v\\${SGE_TASK_ID}_${genome}_txdb <- gencode_txdb(\\${SGE_TASK_ID}, '${genome}')
#
# ## Workaround for an RSQLite::sqliteCopyDatabase() error
# saveDb(gencode_v\\${SGE_TASK_ID}_${genome}_txdb, file = '~/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite')
# system('mv ~/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite gencode/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite')
#
# ## Build and save the annotateTranscripts output
# gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes<- gencode_annotated_genes(gencode_v\\${SGE_TASK_ID}_${genome}_txdb)
# save(gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes, file = 'gencode/gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes.rda')
#
# ## Build and save the GenomicState
# gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState <- gencode_genomic_state(gencode_v\\${SGE_TASK_ID}_${genome}_txdb)
# save(gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState, file = 'gencode/gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState.rda')
#
# ## Reproducibility information
# print('Reproducibility information:')
# Sys.time()
# proc.time()
# options(width = 120)
# session_info()
# ",
# file = 'build_gencode_human_run.R'
# )
## Update the script to run
script <- readLines("build_gencode_human.sh")
script[grepl("Rscript", script)] <- "Rscript -e \"library('GenomicState'); library('AnnotationDbi'); library('sessioninfo'); dir.create('gencode', showWarnings = FALSE); gencode_v\\${SGE_TASK_ID}_${genome}_txdb <- gencode_txdb('\\${SGE_TASK_ID}', '${genome}'); saveDb(gencode_v\\${SGE_TASK_ID}_${genome}_txdb, file = '~/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite'); system('mv ~/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite gencode/gencode_v\\${SGE_TASK_ID}_${genome}_txdb.sqlite'); gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes<- gencode_annotated_genes(gencode_v\\${SGE_TASK_ID}_${genome}_txdb); save(gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes, file = 'gencode/gencode_v\\${SGE_TASK_ID}_${genome}_annotated_genes.rda'); gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState <- gencode_genomic_state(gencode_v\\${SGE_TASK_ID}_${genome}_txdb); save(gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState, file = 'gencode/gencode_v\\${SGE_TASK_ID}_${genome}_GenomicState.rda'); print('Reproducibility information:'); Sys.time(); proc.time(); options(width = 120); session_info()\""
writeLines(script, "build_gencode_human.sh")
## Now run with: sh build_gencode_human.sh
system("sh build_gencode_human.sh")
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 3.6.1 Patched (2019-09-06 r77160)
# os CentOS Linux 7 (Core)
# system x86_64, linux-gnu
# ui X11
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz US/Eastern
# date 2019-10-03
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date lib source
# assertthat 0.2.1 2019-03-21 [2] CRAN (R 3.6.1)
# backports 1.1.4 2019-04-10 [2] CRAN (R 3.6.1)
# cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
# codetools 0.2-16 2018-12-24 [3] CRAN (R 3.6.1)
# colorout * 1.2-2 2019-09-26 [1] Github (jalvesaq/colorout@641ed38)
# colorspace 1.4-1 2019-03-18 [2] CRAN (R 3.6.1)
# crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
# digest 0.6.21 2019-09-20 [1] CRAN (R 3.6.1)
# dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.1)
# ggplot2 3.2.1 2019-08-10 [1] CRAN (R 3.6.1)
# glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
# gtable 0.3.0 2019-03-25 [2] CRAN (R 3.6.1)
# hms 0.5.1 2019-08-23 [2] CRAN (R 3.6.1)
# htmltools 0.3.6 2017-04-28 [2] CRAN (R 3.6.1)
# htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.6.1)
# httpuv 1.5.2 2019-09-11 [1] CRAN (R 3.6.1)
# jsonlite 1.6 2018-12-07 [2] CRAN (R 3.6.1)
# later 0.8.0 2019-02-11 [2] CRAN (R 3.6.1)
# lattice 0.20-38 2018-11-04 [3] CRAN (R 3.6.1)
# lazyeval 0.2.2 2019-03-15 [2] CRAN (R 3.6.1)
# lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.1)
# lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.6.1)
# magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
# munsell 0.5.0 2018-06-12 [2] CRAN (R 3.6.1)
# pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.1)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
# png 0.1-7 2013-12-03 [2] CRAN (R 3.6.1)
# promises 1.0.1 2018-04-13 [2] CRAN (R 3.6.1)
# pryr 0.1.4 2018-02-18 [2] CRAN (R 3.6.1)
# purrr 0.3.2 2019-03-15 [2] CRAN (R 3.6.1)
# R6 2.4.0 2019-02-14 [2] CRAN (R 3.6.1)
# Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.1)
# readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
# rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.1)
# rmote * 0.3.4 2019-09-26 [1] Github (cloudyr/rmote@fbce611)
# scales 1.0.0 2018-08-09 [2] CRAN (R 3.6.1)
# servr 0.15 2019-08-07 [1] CRAN (R 3.6.1)
# sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
# sgejobs * 0.99.0 2019-09-26 [1] Github (LieberInstitute/sgejobs@94a6151)
# stringi 1.4.3 2019-03-12 [2] CRAN (R 3.6.1)
# stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
# tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.1)
# tidyr 1.0.0 2019-09-11 [1] CRAN (R 3.6.1)
# tidyselect 0.2.5 2018-10-11 [2] CRAN (R 3.6.1)
# vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.1)
# withr 2.1.2 2018-03-15 [2] CRAN (R 3.6.1)
# xfun 0.10 2019-10-01 [1] CRAN (R 3.6.1)
# zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.1)
#
# [1] /users/lcollado/R/3.6
# [2] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-3.6/R/3.6/lib64/R/site-library
# [3] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-3.6/R/3.6/lib64/R/library
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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