regis/notes.txt at main · BioinformaticsOnLine/regis · GitHub

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./regis -t paired -m reference -r ../sample/in/GCA_907165135.1_OKI2018_I68_1.0_genomic.fna -g ../sample/in/GCA_907165135.1_OKI2018_I68_1.0_genomic.gff -o rout --f1 ../sample/in/SRR10341223_forward.fastqsanger --f2 ../sample/in/SRR10341223_reverse.fastqsanger

./regis -t paired -m denovo --assembler rnabloom -o rout2 --f1 ../sample/in/SRR10341223_forward.fastqsanger --f2 ../sample/in/SRR10341223_reverse.fastqsanger

./regis -t paired -m reference \
  -r /Users/pranjalpruthi/Documents/GitHub/regis-data/sample/in/GCA_907165135.1_OKI2018_I68_1.0_genomic.fna \
  -g /Users/pranjalpruthi/Documents/GitHub/regis-data/sample/in/GCA_907165135.1_OKI2018_I68_1.0_genomic.gff \
  -o /Users/pranjalpruthi/Documents/GitHub/regis/out_mac_test2 \
  --f1 /Users/pranjalpruthi/Documents/GitHub/regis-data/sample/in/SRR10341223_forward.fastqsanger \
  --f2 /Users/pranjalpruthi/Documents/GitHub/regis-data/sample/in/SRR10341223_reverse.fastqsanger \
  --lnctar-best


CGO_ENABLED=1 CC=/Users/pranjalpruthi/mambaforge/envs/regis_dev/bin/x86_64-apple-darwin13.4.0-clang /Users/pranjalpruthi/mambaforge/envs/regis_dev/bin/go build -o regis;

curl -X POST http://localhost:3000/api/v1/jobs/submit \
  -H "Content-Type: application/json" \
  -H "X-API-Key: <YOUR_KEY_FROM_SERVER_LOG>" \
  -d @local_job.json


./regis -t paired -m reference \
  -r "/home/ajay/Desktop/Workspace_Pranjal/sample/in/GCA_907165135.1_OKI2018_I68_1.0_genomic.fna" \
  -g "/home/ajay/Desktop/Workspace_Pranjal/sample/in/GCA_907165135.1_OKI2018_I68_1.0_genomic.gff" \
  -o "out_linux_test_cli" \
  --f1 "/home/ajay/Desktop/Workspace_Pranjal/sample/in/SRR10341223_forward.fastqsanger" \
  --f2 "/home/ajay/Desktop/Workspace_Pranjal/sample/in/SRR10341223_reverse.fastqsanger" \
  --lnctar-best

conda build . --output-folder ./conda-bld/ -c bioconda -c conda-forge -c jitendralab
CONDA_SUBDIR=osx-64 conda build . --output-folder ./conda-bld/ -c bioconda -c conda-forge -c jitendralab

git add .
git commit -m "Release v1.0.2: Fix asset path resolution for Conda"
git tag v1.0.2
git push origin main --tags

git pull origin main

anaconda upload -u jitendralab ./conda-bld/osx-64/regis-1.0.5-*.tar.bz2

# Step 1: Build the conda package
conda build . --output-folder ./conda-bld/ -c bioconda -c conda-forge -c jitendralab

# Step 2: Upload to Anaconda Cloud (after build completes)
anaconda upload -u jitendralab ./conda-bld/linux-64/regis-1.0.5-*.tar.bz2
or
anaconda upload -u jitendralab ./conda-bld/linux-64/regis-1.0.5-*.conda

# Simple build (uses version from version/version.go)
# If you see "go: no such tool compile" with regis_dev active: unset GOROOT (conda vs Homebrew clash)
unset GOROOT && go build -o regis .
# Or use the helper script (handles GOROOT + version ldflags):
./scripts/build.sh

# regis_dev on Apple Silicon: env is mostly osx-64 (Rosetta). Install bioconda tools with:
#   conda remove -y go _go_select   # if conda install fastp fails on _go_select
#   CONDA_SUBDIR=osx-64 conda install -c bioconda -c conda-forge fastp
# Or pin subdir for the env: conda config --env --set subdir osx-64

# Build with optimizations (smaller binary, stripped debug info)
go build -ldflags="-s -w" -o regis .

# Build with explicit version (like conda does)
go build -ldflags="-s -w -X github.com/BioinformaticsOnLine/regis/version.Version=1.0.5" -o regis .

# Run directly without building
go run .

# Build and verify version
go build -o regis . && ./regis --version

# ─── v1.0.6: Fix libgcc>=15 / glibc solver conflict ─────────────────────────
# IMPORTANT: Build must be done on Linux (or use conda-build on Linux CI)
# The explicit `__glibc >=2.17` virtual package constraint in meta.yaml
# prevents libgcc>=15 injection and ensures compatibility with older and newer glibc.

# ─── Conda publish (regis is NOT noarch — build per platform) ───────────────
# Linux users need linux-64; Mac users need osx-64. Never upload a Mac build as noarch.

# Linux (on a Linux machine or CI):
conda build . --output-folder ./conda-bld/ -c bioconda -c conda-forge -c jitendralab
anaconda upload -u jitendralab ./conda-bld/linux-64/regis-1.1.4-*.tar.bz2

# macOS Apple Silicon / Rosetta (osx-64 bioconda stack):
CONDA_SUBDIR=osx-64 conda build . --output-folder ./conda-bld/ -c bioconda -c conda-forge -c jitendralab
anaconda upload -u jitendralab ./conda-bld/osx-64/regis-1.1.4-*.tar.bz2

# Wrong upload (1.1.4 build 0 noarch) contained a Mach-O binary — remove from channel if present:
# anaconda remove -u jitendralab regis/1.1.4/noarch/regis-1.1.4-0.tar.bz2

# Step 3: Tag the release
git add meta.yaml
git commit -m "Release v1.0.6: Fix libgcc>=15 glibc solver conflict on linux-64"
git tag v1.0.6
git push origin main --tags