guix/gnu/packages/bioinformatics.scm, branch java-team

gnu: ant/java8: Rename to ant.

2026-04-20T06:31:21+00:00

* gnu/packages/java.scm (ant): Rename to...
(ant/java7): ...this.
(ant/java8): Rename to...
(ant): ...this.
(java-qdox-1.12, java-jarjar, java-hamcrest-core, java-hamcrest-parent-pom)
(java-junit, java-org-ow2-parent-pom-1.3, java-asm-bootstrap): Rename
inputs accordingly.
* gnu/packages/axoloti.scm: Rename accordingly.
* gnu/packages/bioinformatics.scm: idem.
* gnu/packages/groovy.scm: idem.
* gnu/packages/java-maths.scm: idem.
* guix/build-system/ant.scm: idem.

Change-Id: I9d79ce8e351862747420fc2a58301b7f61212293

gnu: ant-junit: Deprecate.

2026-04-20T06:31:15+00:00

* gnu/packages/bioinformatics (java-picard-1.113): Remove ant-junit
  dependency.
* gnu/packages/groovy.scm (groovy-ant): Remove ant-junit dependency.
* gnu/packages/java.scm (ant-junit): Deprecate in favor of ant/java8.

Change-Id: Ic877958cc559acd710ac38b7b9d4b271d3982c3f

gnu: Remove mantis.

2026-04-13T10:34:44+00:00

* gnu/packages/bioinformatics.scm (mantis): Delete variable.

Fixes: guix/guix#7055
Change-Id: I4655b0dc2b9de2b3cb5924538d562539454d5240

gnu: r-pando: Update to 1.1.1.

2026-04-10T10:29:51+00:00

* gnu/packages/bioinformatics.scm (r-pando): Update to 1.1.1.
[source]: Update repository URL.
[arguments]: Delete phase 'loosen-requirements.

Change-Id: If3709336de2794da4c16a648137c6538d192c232

gnu: bioparser: Update to 3.1.0.

2026-04-09T13:26:12+00:00

* gnu/packages/bioinformatics.scm (bioparser): Update to 3.1.0.
[source]: Use version tag as commit.
[arguments]<#:phases>: Remove override of check phase. Add phase
to enable testing in CMake instead.

Change-Id: I641481e49bd98d32cae067dde984985a4ad0c5a9
Signed-off-by: Andreas Enge

gnu: biosoup: Update to 0.11.0.

2026-04-09T13:26:12+00:00

* gnu/packages/bioinformatics.scm (biosoup): Update to 0.11.0.
[source]: Use version tag as commit.
[arguments]<#:phases>: Remove override of check phase. Add phase
to enable testing in CMake instead.

Change-Id: I426d1014cf020bbbf15e47c44e2902f823ddd09c
Signed-off-by: Andreas Enge

gnu: Remove circtools.

2026-04-09T13:26:12+00:00

* gnu/packages/bioinformatics.scm (circtools): Delete variable.
* gnu/packages/rust-crates.scm: Remove cargo-inputs for circtools.

Fixes: guix/guix#5313
Change-Id: Ic94e9ba7c1500b018fc71e1a10bc25594af16b92

gnu: Remove ciri-long.

2026-04-09T13:26:11+00:00

* gnu/packages/bioinformatics.scm (ciri-long): Delete variable.

Change-Id: Id1f595a162881e6765cb2fb192ba87740667bd9b

gnu: ravanan: Use git fetch.

2026-04-08T09:51:10+00:00

* gnu/packages/bioinformatics.scm (ravanan)[source]: Switch to
get-fetch.

Change-Id: Icbd58b742a1d5e145b8b071c1708b3ff01c72972

gnu: ravanan: Build with the same Guile as the ‘guix’ package.

2026-04-08T09:32:00+00:00

Fixes a regression introduced in c3fefb065c53703e3dc6507c813182101c5c3a38.

* gnu/packages/bioinformatics.scm (ravanan)[inputs]: Replace ‘guile-3.0’
by a ‘lookup-package-input’ call.

Merges guix/guix!7734

Change-Id: I584bf55ddbf44e3cc13896f2ef48ccc8f305059d
Signed-off-by: Cayetano Santos