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add aarch64 control-freec (debugging) #52018

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add aarch64 control-freec (debugging) #52018

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ff580bd
add arm support for controlfreec
FriederikeHanssen Oct 29, 2024
722fc3e
bump build
rpetit3 Oct 29, 2024
84456c3
Merge branch 'master' into arm_support_cf
mencian Oct 29, 2024
f274933
Update meta.yaml
mencian Oct 29, 2024
719445e
Merge branch 'master' into arm_support_cf
FriederikeHanssen Oct 30, 2024
41fce3d
add debug to build.sh
rpetit3 Oct 30, 2024
70f0502
Merge remote-tracking branch 'rike/arm_support_cf' into arm_support_c…
dslarm Nov 8, 2024
c947991
add debug
dslarm Nov 8, 2024
ff33c95
further debugging
dslarm Nov 8, 2024
3a043fc
more debug
dslarm Nov 8, 2024
25eb4ff
try to execute get_fasta_lengths.pl
dslarm Nov 8, 2024
71da694
more deubg
dslarm Nov 8, 2024
871e5a8
More debug..
dslarm Nov 8, 2024
d37745f
dont ship env - check it exists w whcih
dslarm Nov 8, 2024
4b4b35e
try execute get_fasta_lengths.pl
dslarm Nov 8, 2024
3acab93
does make work on other scripts
dslarm Nov 9, 2024
83f13b8
which isnt working? what is it..
dslarm Nov 9, 2024
31042aa
is it length of scritp name related?
dslarm Nov 9, 2024
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7 changes: 6 additions & 1 deletion recipes/control-freec/build.sh
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
#!/bin/bash

# Debug for ARM build, can remove later
set -x
Comment on lines +2 to +3
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🛠️ Refactor suggestion

Add shell safety flags and plan debug mode cleanup.

While set -x is helpful for debugging ARM builds, consider:

  1. Adding recommended shell safety flags
  2. Removing debug mode once ARM issues are resolved
 #!/bin/bash
-# Debug for ARM build, can remove later
-set -x
+set -euo pipefail
+
+# TODO: Remove after ARM debugging is complete
+if [[ "${CONDA_BUILD_CROSS_COMPILATION:-}" == "1" ]]; then
+    set -x
+fi
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
# Debug for ARM build, can remove later
set -x
#!/bin/bash
set -euo pipefail
# TODO: Remove after ARM debugging is complete
if [[ "${CONDA_BUILD_CROSS_COMPILATION:-}" == "1" ]]; then
set -x
fi


mkdir -p $PREFIX/bin

Expand All @@ -11,5 +12,9 @@ do
cp $f $PREFIX/bin
done

ls -l $PREFIX/bin
echo get_fasta_lengths.pl is...
cat $PREFIX/bin/get_fasta_lengths.pl

cd src
$CXX -o $PREFIX/bin/freec $CXXFLAGS $LDFLAGS *.cpp -lpthread
11 changes: 8 additions & 3 deletions recipes/control-freec/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ source:
- perl_shebang.patch

build:
number: 0
number: 1
run_exports:
- {{ pin_subpackage('control-freec', max_pin="x") }}

Expand All @@ -30,6 +30,8 @@ requirements:

test:
commands:
- ls -l
- ls -l bin
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🛠️ Refactor suggestion

Remove debugging directory listing commands

The ls commands appear to be debugging artifacts and don't contribute to package validation. The existing test commands already properly verify the installation of all components.

  test:
    commands:
-    - ls -l
-    - ls -l bin
     - freec
     - freec2bed.pl
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
- ls -l
- ls -l bin
- freec
- freec2bed.pl

- freec
- freec2bed.pl
- freec2circos.pl
Expand All @@ -42,7 +44,8 @@ test:

about:
home: https://github.com/BoevaLab/FREEC
license: GPL (>=2)
license: GPL-2.0-or-later
license_family: GPL2
summary: |
Copy number and genotype annotation from whole genome and whole exome
sequencing data.
Expand All @@ -54,4 +57,6 @@ extra:
like e.g. freec2bed.pl and freec2circos.pl (see homepage) are available in the
command line as well.
identifiers:
- biotools:freec
- biotools:freec
additional-platforms:
- linux-aarch64
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