Latest master portable build

Automated HiCT portable build from 92e27177c90e19a1dae38916965592cdf9f9b411.

Source: 92e2717
Workflow run: https://github.com/ctlab/HiCT_JVM/actions/runs/27463378197

⚠️ For quick testing, download the exact artifact for your OS:

• Windows: HiCT-1.0.168-79be52c-webui_22e2511-windows-x86_64.exe
• Linux: HiCT-1.0.168-79be52c-webui_22e2511-linux-x86_64.run
  Recommended for most desktop/server Linux systems such as Ubuntu, Debian, Fedora, RHEL, CentOS, openSUSE, Arch, and similar glibc-based distributions. It caches the extracted program next to the downloaded file, so repeated starts usually do less unpacking.
  Run it with: chmod +x HiCT-1.0.168-79be52c-webui_22e2511-linux-x86_64.run and then bash HiCT-1.0.168-79be52c-webui_22e2511-linux-x86_64.run.
• Linux AppImage: HiCT-1.0.168-79be52c-webui_22e2511-x86_64.AppImage
  Use this when the Linux runfile does not start, or on older/minimal Linux systems such as manylinux2010-like environments and Alpine/musl containers. On normal desktop Linux it uses the system loader; if that cannot start the bundled Java runtime, it falls back to its included glibc/ld-linux runtime.
  Run it with: chmod +x HiCT-1.0.168-79be52c-webui_22e2511-x86_64.AppImage and then ./HiCT-1.0.168-79be52c-webui_22e2511-x86_64.AppImage.
  If the AppImage reports a FUSE or mount error, run: APPIMAGE_EXTRACT_AND_RUN=1 ./HiCT-1.0.168-79be52c-webui_22e2511-x86_64.AppImage. This mode is more compatible but may unpack the application to a temporary directory each time.

Linux choice summary:

• Start with the .run file on normal Linux installations.
• Use the AppImage for older systems, Alpine/musl, containers, or if the .run file reports a glibc/runtime error.
• Both Linux packages can start the server from the command line, for example: start-server or start-server --help after the artifact name.
• For a remote SSH cluster, forward both ports from your local computer: ssh -L 8080:127.0.0.1:8080 -L 5000:127.0.0.1:5000 user@cluster.example.org, then run HiCT on the remote machine with start-server and open http://localhost:8080 locally.
• macOS: HiCT-1.0.168-79be52c-webui_22e2511-darwin-arm64.run HiCT-1.0.168-79be52c-webui_22e2511-darwin-x86_64.run
  These are Terminal-run .run files, not .dmg installers. There is no application icon to drag into Applications.
  Open Terminal, go to the download folder, run xattr -d com.apple.quarantine ./HiCT-*.run if macOS blocks the file, then run chmod +x ./HiCT-*.run and ./HiCT-*.run.

See HiCT-1.0.168-79be52c-webui_22e2511-build-origin.txt and HiCT-1.0.168-79be52c-webui_22e2511-release-assets.sha256 for provenance and checksums.

Latest jvm-sfx-native portable build

Automated HiCT portable build from f949d82c2b26a588d4eea456f5496b44fa086883.

Source: f949d82
Workflow run: https://github.com/ctlab/HiCT_JVM/actions/runs/27453067893

⚠️ For quick testing, download the exact artifact for your OS:

• Windows: HiCT-1.0.166-41ca6d3-webui_1a02368-windows-x86_64.exe
• Linux: HiCT-1.0.166-41ca6d3-webui_1a02368-linux-x86_64.run
  Recommended for most desktop/server Linux systems such as Ubuntu, Debian, Fedora, RHEL, CentOS, openSUSE, Arch, and similar glibc-based distributions. It caches the extracted program next to the downloaded file, so repeated starts usually do less unpacking.
  Run it with: chmod +x HiCT-1.0.166-41ca6d3-webui_1a02368-linux-x86_64.run and then bash HiCT-1.0.166-41ca6d3-webui_1a02368-linux-x86_64.run.
• Linux AppImage: HiCT-1.0.166-41ca6d3-webui_1a02368-x86_64.AppImage
  Use this when the Linux runfile does not start, or on older/minimal Linux systems such as manylinux2010-like environments and Alpine/musl containers. On normal desktop Linux it uses the system loader; if that cannot start the bundled Java runtime, it falls back to its included glibc/ld-linux runtime.
  Run it with: chmod +x HiCT-1.0.166-41ca6d3-webui_1a02368-x86_64.AppImage and then ./HiCT-1.0.166-41ca6d3-webui_1a02368-x86_64.AppImage.
  If the AppImage reports a FUSE or mount error, run: APPIMAGE_EXTRACT_AND_RUN=1 ./HiCT-1.0.166-41ca6d3-webui_1a02368-x86_64.AppImage. This mode is more compatible but may unpack the application to a temporary directory each time.

Linux choice summary:

• Start with the .run file on normal Linux installations.
• Use the AppImage for older systems, Alpine/musl, containers, or if the .run file reports a glibc/runtime error.
• Both Linux packages can start the server from the command line, for example: start-server or start-server --help after the artifact name.
• For a remote SSH cluster, forward both ports from your local computer: ssh -L 8080:127.0.0.1:8080 -L 5000:127.0.0.1:5000 user@cluster.example.org, then run HiCT on the remote machine with start-server and open http://localhost:8080 locally.
• macOS: HiCT-1.0.166-41ca6d3-webui_1a02368-darwin-arm64.run HiCT-1.0.166-41ca6d3-webui_1a02368-darwin-x86_64.run
  These are Terminal-run .run files, not .dmg installers. There is no application icon to drag into Applications.
  Open Terminal, go to the download folder, run xattr -d com.apple.quarantine ./HiCT-*.run if macOS blocks the file, then run chmod +x ./HiCT-*.run and ./HiCT-*.run.

See HiCT-1.0.166-41ca6d3-webui_1a02368-build-origin.txt and HiCT-1.0.166-41ca6d3-webui_1a02368-release-assets.sha256 for provenance and checksums.

Latest autogenerated build (branch jvm-hic-converter)

Commits

• 12a4eb9: Merge a4affbe into 7ee7b68 (Alexander Serdyukov)

Latest autogenerated build (branch jvm-api-v1)

Commits

• 331d557: Cosmetic/Usability fixes (Alexander Serdyukov) #19
• bb20b77: Added pixel overlay capabilities (Alexander Serdyukov) #19
• d442da9: Merge bb20b77 into 6a6906a (Alexander Serdyukov)

Latest autogenerated build (branch migrate-converters-update-ui-1dtracks)

Commits

• 6a5926a: Merge 87e372b into 978fda6 (Alexander Serdyukov)

Latest autogenerated build (branch migrate-converters-update-ui)

Commits

• b6a237d: Review/refactor scaffolding operations (Alexander Serdyukov) #15
• 11cdb20: Optimized loading of lots-small-contig regions after regrouping by AGP (Alexander Serdyukov) #15
• 1ce0372: Improved performance in case of lots of small contigs (Alexander Serdyukov) #15
• 47ff0a1: Merge 1ce0372 into 225be46 (Alexander Serdyukov)

Latest autogenerated build (branch migrate-converters)

Commits

• 79edfd6: Scaffolding operations stopped working, converter does unknown stuffm works with Java 21 (Alexander Serdyukov)
• e3b4ef3: JVM-powered converter working, but compression differs (Alexander Serdyukov)
• 4096734: Add support for other compression algorithms to converter (Alexander Serdyukov)
• 93ca650: Tried adding conversion progress tracker (Alexander Serdyukov)
• 781eec2: mcool -> hict.hdf5 converter works and displays status, bugs with bpResolution from WebUI are fixed (Alexander Serdyukov)
• cfba91c: Faster converter from mcool to hict (Alexander Serdyukov)

Latest autogenerated build (branch dev-jhdf5-1.10.11-dynamic-recompilation)

Commits

• d1f2ade: JHDF5.so now has more implementation compiled-in (Aleksandr Serdiukov)

Latest autogenerated build

Commits

• fb72eda: Revert "Another attempt to use re-compiled SiS jHDF5 library with re-compiled HDF5 1.10.11 library from sources with plugin support enabled. Currently only for Windows and Linux." (Aleksandr Serdiukov)