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Dev gene lab reference annotations v gl dppd 7110 a #131

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3f731d5
Create GL-DPPD-7110-A.md
asaravia-butler Apr 25, 2024
98ff3e3
Add files via upload
asaravia-butler Apr 25, 2024
b6d408a
Updating to point to pipeline version A
asaravia-butler Apr 25, 2024
9123f89
[GL_RefAnnotTable] Added rat links and annotation table
torres-alexis May 24, 2024
8d6f239
[GL_RefAnnotTable] Updated Reference annotations CSV
torres-alexis Jun 2, 2024
e27b4c7
[GL_RefAnnotTable] GL_RefAnnotTable-A 1.1.0
torres-alexis Jul 12, 2024
e22158d
[GL_RefAnnotTable] Initial microbes updates
torres-alexis Aug 4, 2024
f6154f7
[GL_RefAnnotTable] GL_RefAnnotTable-A 1.1.0
torres-alexis Aug 12, 2024
9b2b943
[GL_RefAnnotTable] Added makeOrgPackageFromNCBI to DPPD doc
torres-alexis Sep 3, 2024
0020c19
[GL_RefAnnotTable] Adjust DPPD doc
torres-alexis Sep 3, 2024
3dc8f2c
[GL_RefAnnotTable] Change input arg to full name
torres-alexis Sep 4, 2024
97d5fef
Merge pull request #110 from torres-alexis/DEV_GeneLab_Reference_Anno…
asaravia-butler Sep 5, 2024
eb93b05
Adding missing updates
asaravia-butler Sep 5, 2024
bbf7a78
Updating install and run instructions.
asaravia-butler Sep 5, 2024
7c011a2
[GL_RefAnnotTable] Misc fixes
torres-alexis Sep 6, 2024
9fd9fb7
[GL_RefAnnotTable] Typo fixes
torres-alexis Sep 6, 2024
8050e32
[GL_RefAnnotTable] Add database versions, fix go.db version
torres-alexis Sep 6, 2024
d910e55
[GL_RefAnnotTable] Add go.db info
torres-alexis Sep 6, 2024
81d06dd
[GL_RefAnnotTable] Move panther note line
torres-alexis Sep 6, 2024
c72d4bb
Merge pull request #118 from torres-alexis/DEV_GeneLab_Reference_Anno…
asaravia-butler Sep 11, 2024
cc11ff9
Specify DB versions used
asaravia-butler Sep 11, 2024
6299719
Input output updates, remove unnecessary variables
asaravia-butler Sep 11, 2024
8bae3a5
Removed target_species_designation variable
asaravia-butler Sep 11, 2024
c3f621b
[GL_RefAnnotTable] Typo fixes
torres-alexis Sep 11, 2024
65f04bd
Merge pull request #122 from torres-alexis/DEV_GeneLab_Reference_Anno…
asaravia-butler Sep 11, 2024
7228880
Typo fix
asaravia-butler Sep 16, 2024
2749fe5
[GL_RefAnnotTable] Fix R packages, add docker instructions
torres-alexis Sep 16, 2024
c72d704
[GL_RefAnnotTable] Typo fixes
torres-alexis Sep 16, 2024
fab25b4
[GL_RefAnnotTable] Typo fixes
torres-alexis Sep 16, 2024
3e3dec6
[GL_RefAnnotTable] Add Docker/Singularity, fix R lib
torres-alexis Sep 16, 2024
f9c4f03
[GL_RefAnnotTable] Update docker image
torres-alexis Sep 17, 2024
ffec6ae
[GL_RefAnnotTable] Typo fixes
torres-alexis Sep 17, 2024
c4acfad
[GL_RefAnnotTable] Readd comment
torres-alexis Sep 17, 2024
51570c4
[GL_RefAnnotTable] Typo fix
torres-alexis Sep 17, 2024
40e3652
Merge pull request #123 from torres-alexis/DEV_GeneLab_Reference_Anno…
asaravia-butler Oct 1, 2024
4f181bf
Refactor instructions for singularity use
torres-alexis Oct 1, 2024
232e421
[GL_RefAnnotTable] add container + local instructions
torres-alexis Oct 2, 2024
99daa55
[GL_RefAnnotTable] Fix typos
torres-alexis Oct 2, 2024
12b0587
[GL_RefAnnotTable] Fix interactive install-org-db
torres-alexis Oct 2, 2024
86814bd
[GL_RefAnnotTable] switch from apptainer to singularity
torres-alexis Oct 10, 2024
d4b1c09
fix typo
torres-alexis Oct 10, 2024
f839222
[GL_RefAnnotTable] fix .img image name
torres-alexis Oct 10, 2024
0338c93
Merge pull request #125 from torres-alexis/DEV_GeneLab_Reference_Anno…
asaravia-butler Oct 22, 2024
bd917b4
Formatting updates
asaravia-butler Oct 22, 2024
499538d
Formatting updates
asaravia-butler Oct 22, 2024
75dd660
Typo and link fixes
asaravia-butler Oct 22, 2024
f54a529
Formatting updates
asaravia-butler Oct 23, 2024
f015225
remove lib path
torres-alexis Oct 23, 2024
fce6a73
Update GL-DPPD-7110-A_build-genome-annots-tab.R
torres-alexis Oct 23, 2024
3cc61cf
Add possible paths to install-org-db execution function
torres-alexis Oct 23, 2024
8619121
Update GL-DPPD-7110-A_build-genome-annots-tab.R
torres-alexis Oct 23, 2024
8bbf66d
Update GL-DPPD-7110-A.md
torres-alexis Oct 23, 2024
4bec193
Update GL-DPPD-7110-A_build-genome-annots-tab.R
torres-alexis Oct 24, 2024
6da57fa
Updating signature matrix
asaravia-butler Oct 24, 2024
e3dfb4b
Formatting updates
asaravia-butler Oct 24, 2024
d1ea649
remove custom org dbs from annotation table
torres-alexis Oct 29, 2024
f06cf14
move timeout to top of scripts, add to readme
torres-alexis Oct 30, 2024
5088539
add no-home + bind local path to same container path
torres-alexis Oct 30, 2024
6368381
add cols bioconductor_annotations, custom_annotations, change dppd va…
torres-alexis Oct 31, 2024
b39c63c
remove --no-home from readme
torres-alexis Oct 31, 2024
dcdf589
Add r_libs to scrips, readme, standardize notes
torres-alexis Oct 31, 2024
ef2958f
Merge pull request #128 from torres-alexis/DEV_GeneLab_Reference_Anno…
bnovak32 Nov 5, 2024
283c0ab
Update README.md
bnovak32 Nov 8, 2024
c4b100e
Update README.md
bnovak32 Nov 8, 2024
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[GL_RefAnnotTable] Typo fixes
torres-alexis committed Sep 17, 2024

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This commit was created on GitHub.com and signed with GitHub’s verified signature.
commit ffec6ae65236842f50a0a7a5eb3e5ce40c1b8a55
Original file line number Diff line number Diff line change
@@ -301,7 +301,7 @@ if ( file.exists(out_table_filename) ) {
BiocManager::install(target_org_db, ask = FALSE)
if (!requireNamespace(target_org_db, quietly = TRUE)) {
tryCatch({
# Define genus and species regardless of target_org_db
# Parse organism's name in the reference table to create the org.db name (target_org_db)
genus_species <- strsplit(target_organism, " ")[[1]]
if (length(genus_species) < 1) {
stop("Species designation is not correctly formatted: ", target_organism)
Original file line number Diff line number Diff line change
@@ -8,7 +8,7 @@ install_annotations <- function(target_organism, refTablePath) {
filter(species == target_organism) %>%
pull(taxon)

# Define genus and species regardless of target_org_db
# Parse organism's name in the reference table to create the org.db name (target_org_db)
target_species_designation <- ref_table %>%
filter(species == target_organism) %>%
pull(species) %>%