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feat: update delly container #950

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merged 3 commits into from
Jun 9, 2022
Merged

feat: update delly container #950

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2944b82
update changelog
khurrammaqbool Jun 9, 2022
d7a7767
update delly
khurrammaqbool Jun 9, 2022
c9d0f58
add command to container tests
khurrammaqbool Jun 9, 2022
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3 changes: 2 additions & 1 deletion BALSAMIC/containers/delly/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ RUN apt-get update && apt-get install -y \
libncurses-dev \
liblzma-dev \
zlib1g-dev \
bcftools \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*

Expand All @@ -34,7 +35,7 @@ ENV OMP_NUM_THREADS 2
RUN cd /opt \
&& git clone --recursive https://github.com/dellytools/delly.git \
&& cd /opt/delly/ \
&& git checkout v0.9.1 \
&& git checkout v1.0.3 \
&& make STATIC=1 PARALLEL=1 all \
&& make install \

2 changes: 1 addition & 1 deletion BALSAMIC/containers/delly/delly.yaml
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@@ -1 +1 @@
- delly=0.9.1
- delly=1.0.3
4 changes: 3 additions & 1 deletion CHANGELOG.rst
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Expand Up @@ -5,7 +5,7 @@ Added:
^^^^^^

* New option `analysis-workflow` to balsamic config case CLI https://github.com/Clinical-Genomics/BALSAMIC/pull/932
* Delly TIDDIT and vcf2cytosure for WGS https://github.com/Clinical-Genomics/BALSAMIC/pull/947
* `Delly` `TIDDIT` `vcf2cytosure` and method to process SVs and CNVs for WGS https://github.com/Clinical-Genomics/BALSAMIC/pull/947

Changed:
^^^^^^^^
Expand All @@ -15,6 +15,8 @@ Changed:
* QC-workflow for panel cases to be run only with `balsamic-qc` https://github.com/Clinical-Genomics/BALSAMIC/pull/942
* `get_snakefile` function takes the argument `analysis_workflow` to trigger the QC workflow when necessary https://github.com/Clinical-Genomics/BALSAMIC/pull/942
* `bcftools_counts` input depending on `analysis_workflow` https://github.com/Clinical-Genomics/BALSAMIC/pull/942
* Update `delly` to v1.0.3 https://github.com/Clinical-Genomics/BALSAMIC/pull/950


Fixed:
^^^^^^
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2 changes: 1 addition & 1 deletion container_tests/delly/delly.sh
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@@ -1,7 +1,7 @@
#!/bin/bash
# Test if commands exist

valid_commands=( "delly" )
valid_commands=( "delly" "bcftools" )

for valid_command in "${valid_commands[@]}"
do
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2 changes: 1 addition & 1 deletion container_tests/varcall_py3/varcall_py3.sh
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@@ -1,7 +1,7 @@
#!/bin/bash
# Test if commands exist

valid_commands=( "bcftools" "samtools" "tabix" "vardict" "vardict-java" "svdb")
valid_commands=( "bcftools" "samtools" "tabix" "vardict" "vardict-java" "svdb" "bwa" "tiddit")

for valid_command in "${valid_commands[@]}"
do
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