Update HAF-pipe for more robustness

moiexpositoalonsolab · Dec 17, 2024 · d4f6516 · d4f6516
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diff --git a/packages/README.md b/packages/README.md
@@ -5,8  5,8 @@ This directory contains packages (external dependencies) of grenepipe
 that are not available via the conda package manager (i.e., are not on conda-forge or bioconda).
 We currently include
 
- - [HAFpipe](https://github.com/petrov-lab/HAFpipe-line), to be downloaded into `hafpipe`
- - [harp](https://bitbucket.org/dkessner/harp/), to be downloaded into `harp`
  - [HAFpipe](https://github.com/lczech/HAF-pipe), to be downloaded into `hafpipe`. Note that we use our own form, which contains several improvements over the original [HAFpipe-line](https://github.com/petrov-lab/HAFpipe-line).
  - [harp](https://bitbucket.org/dkessner/harp/), to be downloaded into `harp`. Here, we only need the binary, and do not need the repository to be cloned.
 
 Calling
 

diff --git a/packages/setup-hafpipe.sh b/packages/setup-hafpipe.sh
@@ -108,7  108,7 @@ if [ ! -f "${HAFPIPE_BIN}" ] ; then
     # Our improved version
     HAFPIPE_USER="lczech"
     HAFPIPE_REPO="HAF-pipe"
-    HAFPIPE_HASH="ef09729327bd305bdc36cb9e34462a9c85da4f75"
     HAFPIPE_HASH="a96c8293344683523b66590bf1450587ee13a76c"
 
     # Somehow, curl from GitHub works differently - the output is already put into a file,
     # and we get a warning "Warning: Got more output options than URLs" when specifying `-o`,