Skip to content

Latest commit

 

History

History
198 lines (156 loc) · 9.41 KB

ChangeLog.md

File metadata and controls

198 lines (156 loc) · 9.41 KB
Raw

Changelog

CustardPy

2.0.0 (2024-5-22)

  • Changed Python environment from conda to micromamba (/opt/micromamba)
  • Updated Python from 3.8.17 to 3.10.13
  • Install HiCLift

1.9.1 (2024-04-04)

  • Updated HiC1Dmetrics from v0.2.9 to v0.2.10
  • Omitted ${juiceDir}/scripts/common/check.sh which checks the number of ${outputdir}/merged_sort.txt, ${outputdir}/merged_nodups.txt, ${outputdir}/dups.txt and ${outputdir}/opt_dups.txt.

1.9.0 (2024-03-21)

  • Updated distance_vs_count.Juicer and distance_vs_count.Juicer.log to use minimum Q-value threshold of 30 and window size 50 kbp by default
  • Updated plot_distance_count.R to set the background color to white
  • Updated plot_distance_count.log.R to set the background color to white and limit the x- and y-axes
  • Added plot_distance_count_all.R, plot_distance_count_all.log.R, plot_distance_count_multi.R, plot_distance_count_multi.log.R
  • Modified juicer_pigz.sh and juicer_unpigz.sh to compress/uncompress aligned/dups.txt, aligned/opt_dups.txt and aligned/collisions*txt as well
  • makeEigen.sh: Fixed the bug where the computation would not finish if the computation of PC1 in h1d failed.
  • Fixed a bug where pairtools was not found.
  • Added CALDER2
  • Updated chromap from v0.2.4 to v0.2.6
  • Updated bedtools from v2.30.0 to v2.31.0

1.8.0 (2024-03-03)

  • Major Update: If you experience any problems with this version, try the previous version (v1.7.2) and compare the results. If the problem persists, please report it to GitHub issues.
  • The scripts in juicer/scripts/common used in Juicer were replaced to the original C codes and the computational time of Juicer is dramatically improved.
    • Replaced chimeric_blacklist.awk with Juicer_chimeric_blacklist
    • Replaced dups.awk with Juicer_remove_duplicate
    • Replaced fragment.pl with Juicer_fragment
    • Replaced statistics.pl with Juicer_statistics
  • During this improvement I found a bug in chimeric_blacklist.awk where the names of non-autosomes (e.g. chrX and chrY) were not distinguished. This bug has been fixed in the new Juicer_chimeric_blacklist.
    • This bug seems to be related to the new version of Juicer, which uses the chromosome names chr1,chr2,chr3, not 1,2,3. I have confirmed that the output of Juicer_chimeric_blacklist is identical to the older Juicer.
  • Added the Jupyter notebooks for the CustardPy API in the tutorial/ directory.
  • Added the notebooks to the Manual.
  • Updated HiC1Dmetrics from v0.2.5 to v0.2.9

1.7.2 (2024-02-03)

  • Modified gethg38genome.sh and getmm39genome.sh to also create the genometable file.
  • Bug fix in samtools installation
  • Updated SAMtools from 1.17 to 1.19.2
  • Updated SRAtoolkit from 3.0.2 to 3.0.10
  • Change WORKDIR from /opt to /home/ubuntu
  • Installed sudo

1.7.1 (2024-01-23)

  • Modified gethg38genome.sh and getmm39genome.sh to also download the refFlat data.

1.7.0 (2024-01-07)

  • Fixed the bug in plotHiCfeature where TADs and loops were not being rendered
  • Removed the restriction site directories of Juicer and Cooler from this repository to reduce the size
  • Added generate_binlist_from_gtfile.py for 3DChromatin_ReplicateQC analysis
  • Added 07.QualityCheck.sh in tutorial/Hi-C

1.6.0 (2024-01-06)

1.5.0 (2023-12-18)

  • AluI restriction enzyme for BAT Hi-C added to Juicer and Cooler

1.4.5 (2023-12-01)

  • Removed LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/compat/:/usr/local/cuda/lib64
  • Bug fix for HICCUPS error (CUDA not detected)

1.4.4 (2023-11-28)

  • Added -o option to custardpy_process_hic, custardpy_cooler_subfunc.sh, makeMatrix_intra.sh, call_HiCCUPS.sh and juicer_callTAD.sh

1.4.3 (2023-11-05)

  • Added Juicerstats.sh to summarize the mapping stats of Juicer
  • Added Coolerstats.sh to summarize the mapping stats of Cooler

1.4.2 (2023-10-24)

  • Added LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/compat/:/usr/local/cuda/lib64

1.4.1 (2023-9-23)

1.4.0 (2023-8-01)

  • Bug fix for HOMER installation in Dockerfile
  • Changed the parameter of BWA MEM from -SP to -5SP

1.3.1 (2023-7-08)

  • Changed the name of output directory for custardpy_juicer, custardpy_cooler_HiC, and custardpy_cooler_MicroC

1.3.0 (2023-7-06)

  • Modified custardpy_cooler_HiC and custardpy_cooler_MicroC to allow multiple FASTQ files
  • Changed the name of output directory for custardpy_juicer, custardpy_cooler_HiC, and custardpy_cooler_MicroC
  • Modified options of Pairtools according to the tutorial
  • Added python-FIREcaller
  • Added the restriction files of Cooler for various genome builds and enzymes (see the help of custardpy_cooler_HiC)
  • Bug fix: Wrong PATH of pairsqc.py

1.2.0 (2023-6-11)

  • Added 3DChromatin_ReplicateQC
  • Added run_3DChromatin_ReplicateQC.sh for executing 3DChromatin_ReplicateQC
  • Updated custardpy_cooler_HiC and custardpy_cooler_MicroC

1.1.1 (2023-06-07)

  • Added GENOVA
  • Added calculate_compartment_strength command to calculate compartment strength
  • Added HiCUP
  • Bug fix of pairtools and numpy version conflict

1.1.0 (2023-05-24)

  • Added DEG_boundary_analysis command for TAD-proximity analysis
  • Added custardpy_clustering_boundary command for clustering TAD boundaries
  • Added custardpy_differential_DRF command for differential DRF analysis
  • Added calculate_compartment_strength command for calculating compartment strength
  • Bug fix in makeEigen.sh
  • Changed name of custardpy_mappingHiC to custardpy_cooler_HiC
  • Changed name of custardpy_mappingMicroC to custardpy_cooler_MicroC

1.0.0 (2023-05-17)

  • Major Release!

  • Merged the GitHub repositories for CustardPy (this site) and Docker_CustardPy into a single repository.

  • Unified the Docker images for CustardPy and CustardPy_Juicer. Version 1 of the CustardPy docker image now supports all analyses previously offered by CustardPy and CustardPy_Juicer, rendering the latter unnecessary.

  • Docker Image Specifications:

    • OS: Ubuntu 20.04
    • CUDA: cuda11.0.3
    • cuDNN: v8
    • R: 4.3
    • Python: 3.9.13
    • OpenJDK v17
    • Juicer v1.6
    • Juicer tools v1.22.01

Note: CustardPy does not support Juicer Tools v2 due to incompatibility with the .cool file format.

  • Added tools

  • Merged drawTriangleRatioMulti to plotHiCfeature

  • Fixed the error "QStandardPaths: XDG_RUNTIME_DIR points to non-existing path '/run/user/1000', please create it with 0700 permissions." when calculating PC1.

  • Removed /root/.cpanm/work directory

0.4.1 (2023-02-24)

  • Added libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-render-util0 libraries to avoid an error 'qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.'

0.4.0 (2023-01-26)

  • Updated R from 3.6 to 4.2
  • Added FitHiC
  • Added ChIAPop for ChIA-PET analysis

0.3.0 (2022-10-28)

  • Downgraded pairtools from v1.0.1 to v0.3.0

0.2.0 (2022-08-31)

  • Public release
  • Bug Fix for visualization
  • Updated Manual

0.1.0

  • First commit

Docker_CustardPy_Juicer (deprecated)

0.4.0 (2023-04-25)

  • Changed OS from Ubuntu16.06 to Ubuntu20.04
  • Changed CUDA driver from v8 to 11.0.3

0.3.2 (2023-02-07)

  • Change the upper limit of memory in Java from -Xmx32768m to -Xmx128768m

0.3.1 (2022-12-12)

  • Modify mega.sh to adjust CustardPy_juicer
  • Added juicer_genhic.sh that generates a .hic file from the mapped data
  • Deprecated juicer_postprocessing.sh

0.3.0 (2022-10-27)

  • Downgrade juicer_tools from juicer_tools.2.13.07.jar to juicer_tools.1.22.01.jar to keep the consistency between .hic and .cool (see deeptools/HiCExplorer#798)

0.2.0 (2022-08-31)

  • Added restriction sites for Arima and Sau3AI
  • Added restriction sites for various species
  • change R installation from conda to apt

0.1.0

  • First commit