0.12.0 Release #304

donaldcampbelljr · 2025-01-14T21:10:02Z

[0.12.0] -- 2025-01-16

Remove containers from build and docs (docker and singularity)
update native install and bulker install docs
update to the newest versions of Looper (2.0.0), Pipestat (0.12.0), Pypiper (piper == 0.14.3)
update bowtie2, bedtools, fastqc, pigz versions.
replace bamSitesToWig step with gtars uniwig.

for most of the systems the timeout of the download.file() needs to be increased

Update run-conda.md

This reverts commit 1a3d2d1.

Upgrade to newest looper, pipestat

This reverts commit 08b2845.

wigToBigWig, bigWigCat

…at results file

Update containers (bulker, conda, docker)

This reverts commit e19358d.

sunta3iouxos and others added 30 commits August 30, 2024 11:47

Update run-conda.md

3201890

for most of the systems the timeout of the download.file() needs to be increased

update gitignore to contain tutorial file examples

0dd9a1b

update tutorial interfaces and looper config to use looper 2.0

69f804b

update pep versions and remove unused pep names

dd8083d

update pipelines to use proper pipestat_record_identifier argument

12eee9c

re-add PEP names as porject pipeline requires it

d8da6af

Merge pull request #283 from sunta3iouxos/patch-1

6832b85

Update run-conda.md

remove -B flag for preseq and add instructions for preseq 3.2.0

1a3d2d1

update bed tools version

e82000b

Revert "remove -B flag for preseq and add instructions for preseq 3.2.0"

8d3b171

This reverts commit 1a3d2d1.

update bowtie 2.5.4 instructions

aa1175a

update for newest version of samtools

a0181e6

update fastqc version

be8c0c2

correct pigz version

fd1cf28

update requirements, remove divvy as it is now inlcuded with looper

bcc540f

Merge pull request #287 from databio/master_drc_upgrade

2140de3

Upgrade to newest looper, pipestat

update pipeline interfaces to new bulker, and adopt new looper terms

07f5ccb

update output_schema to Trim_loss_rate

6be1602

Initial attempt at replacing bamSitesToWig with gtars workflow

c864a7a

change ints to strs

69e294b

fix headers and targets for pm.run

86930c5

add uniwig command to gtars cmd build

92c0bdf

changes based on updated gtars uniwig 0.1.2

ec4b760

changes based on updated gtars uniwig 0.1.2

198d5d7

step size to 5, smooth to 25 to match bamsitestowig

c4c41b4

add smooth size to bed output

08b2845

Revert "add smooth size to bed output"

d8dbde2

This reverts commit 08b2845.

reduce step size to 1

4c07edb

add scaling back to pipeline for rust uniwig

9730960

fix assigning scaling to cmd string

f596168

donaldcampbelljr added 29 commits January 7, 2025 11:06

remove docker and singularity builds and information

f69a5d7

remove unnecessary tools:

2bfd64c

wigToBigWig, bigWigCat

update conda requirements-conda.yml

0d6d580

change gtars call

6827299

add rust-gtars to conda requirements-conda.yml

1c429fd

update test and tutorials and examples to use looper 2.0.0 and Pipest…

9e97eaa

…at results file

update pepatac bulker docs

a65dada

re-add ucsc-bedgraphtobigwig

521d2a6

re-add ucsc-bigwigmerge

9ce083e

adjust README.md

abe5dc3

update requirements

4d39c3d

update pepatac version and changelog.md

9e51f19

Merge pull request #303 from databio/dev_update_containers

d0afe85

Update containers (bulker, conda, docker)

add gtars to checkinstall

e88b15f

Merge branch 'master' into dev

8ac56c7

change detailed install to reference macs3, update to newest pep links

0f834ca

Merge remote-tracking branch 'origin/dev' into dev

15384d3

redo microtest

38bcc3a

update genome

ed160e3

add 2nd microtest with diff options

9b0f704

update microtest results path

2e048c7

adjust trimmomatic and picard paths

e19358d

Revert "adjust trimmomatic and picard paths"

67a2166

This reverts commit e19358d.

update microtest README.md

f07d9d0

update bulker docs

36dd2b8

update changelog for v0.12.0 release

34bda53

update detailed installation

2f0ddb8

update gold tutorial README.md

9a8918b

update error message in pipeline regarding gtars

7a2e472

donaldcampbelljr merged commit 0d1aad0 into master Jan 16, 2025

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0.12.0 Release #304

0.12.0 Release #304

donaldcampbelljr commented Jan 14, 2025 •

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0.12.0 Release #304

0.12.0 Release #304

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donaldcampbelljr commented Jan 14, 2025 • edited Loading

[0.12.0] -- 2025-01-16

donaldcampbelljr commented Jan 14, 2025 •

edited

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