is recount3 server down?
Closed this issue · 4 comments
ahdee commented
Hi,
I'm trying to download the blood dataset however I've been getting the same error since last week.
library ( recount3)
human_projects <- available_projects()
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
I also tried manually downloading but the link provided would just fail. I also did this in R and got the same error.
https://jhubiostatistics.shinyapps.io/recount3-study-explorer/
recount3::create_rse_manual(
project = "BLOOD",
project_home = "data_sources/gtex",
organism = "human",
annotation = "gencode_v29",
type = "gene"
)
can someone help? thank you.
lcolladotor commented
Hi!
Thanks for your interest in our software.
Thanks for the PR / issue. A close family of mine was diagnosed with cancer, so my availability is limited right now.
It might take me a few weeks to reply properly.
Best,
Leo
lcolladotor commented
Hi @ahdee,
What recount3 version are you using? It does work for me as you can see below.
> recount3::create_rse_manual(
+ project = "BLOOD",
+ project_home = "data_sources/gtex",
+ organism = "human",
+ annotation = "gencode_v29",
+ type = "gene"
+ )
2022-11-01 17:31:33 downloading and reading the metadata.
2022-11-01 17:31:33 caching file gtex.gtex.BLOOD.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/OD/BLOOD/gtex.gtex.BLOOD.MD.gz'
|======================================================================| 100%
2022-11-01 17:31:34 caching file gtex.recount_project.BLOOD.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/OD/BLOOD/gtex.recount_project.BLOOD.MD.gz'
|======================================================================| 100%
2022-11-01 17:31:34 caching file gtex.recount_qc.BLOOD.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/OD/BLOOD/gtex.recount_qc.BLOOD.MD.gz'
|======================================================================| 100%
2022-11-01 17:31:35 caching file gtex.recount_seq_qc.BLOOD.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/metadata/OD/BLOOD/gtex.recount_seq_qc.BLOOD.MD.gz'
|======================================================================| 100%
2022-11-01 17:31:35 downloading and reading the feature information.
2022-11-01 17:31:36 caching file human.gene_sums.G029.gtf.gz.
adding rname 'http://duffel.rail.bio/recount3/human/annotations/gene_sums/human.gene_sums.G029.gtf.gz'
|======================================================================| 100%
2022-11-01 17:31:37 downloading and reading the counts: 1048 samples across 64837 features.
2022-11-01 17:31:37 caching file gtex.gene_sums.BLOOD.G029.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/gtex/gene_sums/OD/BLOOD/gtex.gene_sums.BLOOD.G029.gz'
|======================================================================| 100%
2022-11-01 17:31:50 construcing the RangedSummarizedExperiment (rse) object.
class: RangedSummarizedExperiment
dim: 64837 1048
metadata(8): time_created recount3_version ... annotation recount3_url
assays(1): raw_counts
rownames(64837): ENSG00000278704.1 ENSG00000277400.1 ...
ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
rowData names(10): source type ... havana_gene tag
colnames(1048): GTEX-R55C-0005-SM-3GAE9.1 GTEX-QMR6-0005-SM-32PKY.1 ...
GTEX-1NSGN-0005-SM-DKPPX.1 GTEX-1QP29-0005-SM-DLZQX.1
colData names(198): rail_id external_id ... recount_seq_qc.errq
BigWigURL
> options(width = 120)
> sessioninfo::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23)
os macOS Ventura 13.0
system aarch64, darwin20
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2022-11-01
pandoc 2.17.1.1 @ /opt/homebrew/bin/pandoc
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
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Biobase 2.56.0 2022-04-26 [1] Bioconductor
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BiocGenerics 0.42.0 2022-04-26 [1] Bioconductor
BiocIO 1.6.0 2022-04-26 [1] Bioconductor
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curl 4.3.3 2022-10-06 [1] CRAN (R 4.2.1)
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DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
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Matrix 1.5-1 2022-09-13 [1] CRAN (R 4.2.0)
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Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
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[1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────ahdee commented
What
recount3version are you using? It does work for me as you can see below.
that must be it then, my version is 1.0.7 looks like you are using 1.6
I will upgrade.
thank you.
lcolladotor commented
Hi again,
If you are a Windows user, duffel now fully works on that operating system. That is, the duffel access issue has now been addressed by the internal switch from RCurl::url.exists() to httr::http_error(). You can gain access to these updates by installing recount3 version 1.10.2 (bioc-release aka 3.17) or 1.11.2 (bioc-devel aka 3.18).
duffel currently points to https://registry.opendata.aws/recount/ instead of IDIES.
Best,
Leo