Comments (4)
KimBioInfoStudio
commented on June 2, 2024
we have NOT got a Apple Silicon for test, but we believe that our code could run on it, could you try but the binary from source code? here is the documents for build it from soure https://github.com/OpenGene/fastp?tab=readme-ov-file#or-compile-from-source
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annajbott
commented on June 2, 2024
Might be a different problem but I was having the same error message with conda trying to install fastp. I ran:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority flexible
And this seemed to fix the problem I was having.
conda create -n fastp_test -c bioconda fastp=0.23.4
and
conda create -n fastp_test bioconda::fastp=0.23.4
worked and installed fastp successfully
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ranijames
commented on June 2, 2024
@annajbott Thanks for sharing the steps. Unfortunately, none of these steps worked for me.
After running all config add, I then tried this one liner to install fastp:
conda create -n fastp_test -c bioconda fastp=0.23.4
which threw me the old error,
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- fastp=0.23.4
Current channels:
- https://conda.anaconda.org/bioconda/osx-arm64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/osx-arm64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/osx-arm64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-arm64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
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ranijames
commented on June 2, 2024
@KimBioInfoStudio Sorry for the delayed response,
I have tried the step 1, step 2, step 3. Those steps did not work for me from step 1 onwards. For example, this is the error for step 1:
autogen.sh: line 3: autoreconf: command not found
clang: error: unsupported option '-print-multi-os-directory'
clang: error: no input files
----------------------------------------------------------------
Initialized build system. For a common configuration please run:
----------------------------------------------------------------
./configure --prefix=/usr --libdir=/usr/lib
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Related Issues (20)
- I obtained different 'insert size peaks' when I used different options for the same paired-end sequencing sample.
- Insert size estimation and report interpretation HOT 2
- fastp in my pip package
- aborted core dumped
- Can fastp draw PNG format?
- Very short fragments
- No mouse ouver in kmer matrix
- Can fastq remove read sequences with duplicate IDs?
- Feature request: add option to set lower limit of unqualified quality
- Missing most reads after given r2 adapter HOT 1
- Interpretation help file?
- Store duplicate reads
- Split interleaved output
- interleaved output is not reproducible with multiple threads HOT 1
- Keep occurred error message from the beginning < igzip: invalid gzip header found >
- Nanopore data filtering using fastp HOT 1
- No adapter detected for read and Q20 bases: 4747174600(99.9999%)
- fastp not removing all Illumina universal adapter sequences as indicated by FastQC HOT 4
- few options throw 'undefined error' -reg
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