From 54bb3a6822584d2901d78ee71f203bd3d3dc5f94 Mon Sep 17 00:00:00 2001 From: bio-boris Date: Tue, 3 Aug 2021 14:53:55 -0500 Subject: [PATCH 1/5] Testing upgrade ver and refdata dl --- Dockerfile | 9 ++++----- RELEASE_NOTES.md | 5 +++++ bbmap_version | 2 +- kbase.yml | 2 +- scripts/load_reference_data.sh | 2 +- 5 files changed, 12 insertions(+), 8 deletions(-) diff --git a/Dockerfile b/Dockerfile index d0515e3..37f0670 100644 --- a/Dockerfile +++ b/Dockerfile @@ -16,9 +16,7 @@ ENV NSLOTS 4 WORKDIR /kb/module -# copy everything in, we need the version file -COPY ./ /kb/module - +ENV BBMAP_VERSION=38.91 # add SAMTools (don't need yet) #RUN apt-get update && apt-get install -y samtools @@ -29,8 +27,7 @@ COPY ./ /kb/module # install BBTools -RUN BBMAP_VERSION=$(cat /kb/module/bbmap_version) \ - && BBMAP=BBMap_$BBMAP_VERSION.tar.gz \ +RUN BBMAP=BBMap_$BBMAP_VERSION.tar.gz \ && wget -O $BBMAP https://sourceforge.net/projects/bbmap/files/$BBMAP/download \ && tar -xf $BBMAP \ && rm $BBMAP @@ -43,6 +40,8 @@ RUN cd /kb/module/bbmap/jni \ RUN mkdir /global COPY data/rqc_data/global /global +#copy everything in +COPY ./ /kb/module RUN mkdir -p /kb/module/work RUN chmod -R a+rw /kb/module diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 5cbbc61..2d193a7 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -1,3 +1,8 @@ +### Version 1.0.2 +__Changes__ +- Update BBMap v38.91 (released 2021-07-19) + + ### Version 1.0.1 __Changes__ - Added config options and html results to BBMap diff --git a/bbmap_version b/bbmap_version index 281ca8b..8f109c7 100644 --- a/bbmap_version +++ b/bbmap_version @@ -1 +1 @@ -38.73 +38.91 diff --git a/kbase.yml b/kbase.yml index 20f8cb8..ee8e68c 100644 --- a/kbase.yml +++ b/kbase.yml @@ -14,4 +14,4 @@ owners: [msneddon, wjriehl, dylan] data-version: - 0.3 + 0.3.1 diff --git a/scripts/load_reference_data.sh b/scripts/load_reference_data.sh index 4599c44..ac6bce7 100755 --- a/scripts/load_reference_data.sh +++ b/scripts/load_reference_data.sh @@ -2,7 +2,7 @@ # data directory is always mounted in the /data -BBMAP_VERSION=38.73 +#BBMAP_VERSION=38.73 check_exists() { if ! [ -d $1 ] ; then From 33d0dda3437fb02e10bea3b41bfb6a3109dd7830 Mon Sep 17 00:00:00 2001 From: bio-boris Date: Tue, 3 Aug 2021 15:14:27 -0500 Subject: [PATCH 2/5] Update UI --- ui/narrative/methods/RQCFilter/display.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ui/narrative/methods/RQCFilter/display.yaml b/ui/narrative/methods/RQCFilter/display.yaml index 4b3d69e..06cfbcc 100644 --- a/ui/narrative/methods/RQCFilter/display.yaml +++ b/ui/narrative/methods/RQCFilter/display.yaml @@ -1,7 +1,7 @@ # # define display information # -name: Run the JGI RQCFilter pipeline (BBTools v38.73) +name: Run the JGI RQCFilter pipeline (BBTools v38.91) tooltip: | Runs the JGI reads data preprocessing pipeline From dc1a714d5881a1674faa45d97b31431f1cb1ad17 Mon Sep 17 00:00:00 2001 From: bio-boris Date: Tue, 3 Aug 2021 15:23:53 -0500 Subject: [PATCH 3/5] Follow redirect --- scripts/load_reference_data.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/load_reference_data.sh b/scripts/load_reference_data.sh index ac6bce7..50d93ee 100755 --- a/scripts/load_reference_data.sh +++ b/scripts/load_reference_data.sh @@ -31,7 +31,7 @@ cd /data # Fetch the monster compilation of reference data that Brian Bushnell set up. echo "Downloading RQCFilterData from NERSC Portal" -safe_execute "wget --no-verbose http://portal.nersc.gov/dna/microbial/assembly/bushnell/RQCFilterData.tar" "failed to download reference data!" +safe_execute "wget -L --no-verbose http://portal.nersc.gov/dna/microbial/assembly/bushnell/RQCFilterData.tar" "failed to download reference data!" safe_execute "tar -xf RQCFilterData.tar -C /data" "failed to untar reference data!" safe_execute "rm -f RQCFilterData.tar" "failed to remove reference data!" check_exists /data/RQCFilterData From 3ac9066b9f0c16141455678d7122aa872e6c0596 Mon Sep 17 00:00:00 2001 From: bio-boris Date: Tue, 3 Aug 2021 15:30:12 -0500 Subject: [PATCH 4/5] Update wget to follow redirect --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index 37f0670..380195a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,6 +13,8 @@ MAINTAINER KBase Developer ENV NSLOTS 4 # ----------------------------------------- +RUN apt-get update +RUN apt-get install wget -y WORKDIR /kb/module From 84f853f026d069be91d28e7c339ab2cc32a56f2c Mon Sep 17 00:00:00 2001 From: bio-boris Date: Tue, 3 Aug 2021 15:34:33 -0500 Subject: [PATCH 5/5] Turns out it was https --- Dockerfile | 3 --- scripts/load_reference_data.sh | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 380195a..030ea69 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,9 +13,6 @@ MAINTAINER KBase Developer ENV NSLOTS 4 # ----------------------------------------- -RUN apt-get update -RUN apt-get install wget -y - WORKDIR /kb/module ENV BBMAP_VERSION=38.91 diff --git a/scripts/load_reference_data.sh b/scripts/load_reference_data.sh index 50d93ee..cbb0f82 100755 --- a/scripts/load_reference_data.sh +++ b/scripts/load_reference_data.sh @@ -31,7 +31,7 @@ cd /data # Fetch the monster compilation of reference data that Brian Bushnell set up. echo "Downloading RQCFilterData from NERSC Portal" -safe_execute "wget -L --no-verbose http://portal.nersc.gov/dna/microbial/assembly/bushnell/RQCFilterData.tar" "failed to download reference data!" +safe_execute "wget -L --no-verbose https://portal.nersc.gov/dna/microbial/assembly/bushnell/RQCFilterData.tar" "failed to download reference data!" safe_execute "tar -xf RQCFilterData.tar -C /data" "failed to untar reference data!" safe_execute "rm -f RQCFilterData.tar" "failed to remove reference data!" check_exists /data/RQCFilterData