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PUBLIC-1623 Diagnosis Attempt #41

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PUBLIC-1623 Diagnosis Attempt #41

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54bb3a6
Testing upgrade ver and refdata dl
Aug 3, 2021
33d0dda
Update UI
Aug 3, 2021
dc1a714
Follow redirect
Aug 3, 2021
3ac9066
Update wget to follow redirect
Aug 3, 2021
84f853f
Turns out it was https
Aug 3, 2021
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10 changes: 4 additions & 6 deletions Dockerfile
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Expand Up @@ -13,12 +13,9 @@ MAINTAINER KBase Developer
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
Expand All @@ -29,8 +26,7 @@ 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
Expand All @@ -43,6 +39,8 @@ 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

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5 changes: 5 additions & 0 deletions RELEASE_NOTES.md
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@@ -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
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2 changes: 1 addition & 1 deletion bbmap_version
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@@ -1 +1 @@
38.73
38.91
2 changes: 1 addition & 1 deletion kbase.yml
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Expand Up @@ -14,4 +14,4 @@ owners:
[msneddon, wjriehl, dylan]

data-version:
0.3
0.3.1
4 changes: 2 additions & 2 deletions scripts/load_reference_data.sh
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Expand Up @@ -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
Expand Down Expand Up @@ -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 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
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2 changes: 1 addition & 1 deletion ui/narrative/methods/RQCFilter/display.yaml
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@@ -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
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