16.2.22 UTAP version history

Owned by Dena Leshkowitz
Last updated: 12 Nov, 2023
3 min read

UTAP version 2.0 , 28 august 2023

  1. added ChIP-Seq report

  2. added ATAC-Seq report

  3. added support to Nova-Seq BCL data (Demultiplex from BCL pipeline)

  4. added support to multiple types of clusters (slurm, SGE, LoadLeveler, LSF, PBS)

  5. Added features and corrections to Django Admin site

  6. regenerate STAR indexes, the list is found at : https://bbcunit.atlassian.net/wiki/spaces/BI/pages/1033207870

  7. Added multiple validations to UTAP installation procedure for internal and external users

 

 

UTAP version 1.10.3 , 19 January 2023

1.10.3 UTAP version includes the main following features/changes:

  1. Upgraded OS from ubuntu 14.04.5  LTS (Apr 18 2018)  to ubuntu 22.04  TLS (2022-06-14)

  2. Upgraded web server from Apache/2.4.7 (Ubuntu) to Apache/2.4.52 (Ubuntu)

  3. Python upgraded from python2.7  to python 3.10.6

  4. R upgraded from R  3.3.2 (2016-10-31) to R  4.2.1 (2022-06-23)

  5. Django upgraded to django  4.1.1

  6. Snakemake upgraded from snakemake 3.13.3 to snakemake 7.14.0

  7. All the pipelines software were also upgraded to:

     bcl2fastq-2.20

    bedtools -2.30.0

    bowtie2  -2.5.0

    fastq-multx -1.4.2

    fastqc -0.11.9

    ghostscript - 9.54.0

    homer -4.11

    htseq  -2.0.2

    igvtools  -2.14.1

    macs2  -2.2.7.1

    multiqc  -1.13a

    samtools -1.15.1

    star -2.7.10a

    r-ngsplot  -2.63

  8. Upgraded bbcu home scripts to bbcu-bioutils 1.0.7 and bbcu-ngs-snakemake  1.0.8 

  9. Python ldap upgraded to ldap3  

  10. Added django-python3-ldap for user authentication

  11. Added Cluster submit, status and cancel scripts to snakemake in order to enable snakemake jobscript submission from singularity container to cluster on the host (supportive future for external utap installation)

  12. Added retires and greedy algorithms options to sankemake in order to avoid failed jobs due to cluster memory limitation

 

UTAP version 1.10.1 , 17 November 2021

1.10.1 UTAP version includes the following features/changes:

  1. Added the following modification to NGSplot rule in all transcriptome (RNA-seq and MARS-seq) and chromatin (ChIP-seq and ATAC-seq) pipelines :

    1. running time limitation of one hour

    2. samples limitation to the first 10 samples

    3.  if NGSplot rule fails to run  the pipeline will keep running 

  2. Temporarily (until we will upgrade the R version) removing MA plots generated with Glimma package from the report.

  3. Corrected  uncentered Pearson correlation to centered Pearson correlation in dendrogram and all heatmaps figures

  4. Limiting Single-Cell pipeline usage to BBCU unit only.

  5. Correct the Collaboration path to all class users 

  6. Made e-learning accessible without login. 

  7. Added more validation to the input fastq folder in all pipelines.

  8. Added more validation to the report folder name and to the "run DESeq2 again" folder name 

  9. Fix bugs with ChIP-seq pipeline  

  10. Added scroll bar to large figures in the report.

  11. Added javascript of samples details when choosing input folder in dimultiplex from fastq pipeline 

  12. Correct the number of threads in Single-Cell pipeline

  13. Added Ribo-Seq pipeline (available to BBCU users only)

  14. Remove the send button to the intermine site when the chosen genome is human (need to update the site api for human genome, the old site is no longer available for human genome).

  15. Added UTAP version to all pipelines reports

  16. Corrected phrasing in transcriptome reports 

  17. Converted UTAP to secure site

  18. Add Plasmodium falciparum and Homo sapiens+Plasmodium falciparum genomes 



 UTAP version 1.0.9 includes the following features/changes:

  1. Added a new pipeline: “DESeq from counts matrix“ pipeline (including validation to gene duplication in the uploaded matrix file)

  2. added new genomes and gtf files:

    1. Added Tomato genome version ITAG4  

    2. Added Cannabis sativa (CS10) genome

    3. Updated mm10 mouse gtf files

    4. Updated hg38 human gtf files

  3. improved UTAP internal site documentation.

  4. Provided advanced parameters feature for all users

  5. Provided Single Cell pipeline for all users

  6. Modified and improved ChIP-seq pipeline

  7. Upgraded SC cellRanger to version 4.0.0

  8. Added improvements to report output:

    1. Improved styling of html page

    2. Created dynamic analysis parameters (added details about gtf file version and date, link to yaml parameters file, link to report output folder, link to R sessionInfo, and link to pheno data file).

    3. Added vst calculation when number of samples > 30.

    4. Added data representation with and without batch correction when batch correction is applied.

    5. Added Glimma plots.

    6. Added the corresponding genes lists in the table “Table 2: Links to functional enrichment analysis”.

    7. Changed PCA graph legend - one dot now appears for each sample.

    8. Changed axes ratios of PCA graph so that the graph is now symmetric (square shaped).

    9. Incorporated R rio::export into UTAP to export Excel files.

    10. Added the possibility for users to name the report output folder.



 UTAP version  1.0.8 includes the following features/changes:

  1. Added a new pipeline - ChIP-Seq pipeline.

  2. Added proposed changes in the ATAC-seq pipeline.

  3. Added “advanced parameters” feature to enable customization of selected runtime parameters.

  4. Added progress bar representation for each run

  5. Added the columns “padj.after.FDR.correction” and “pass.after.FDR” to the Deseq_all_results.txt file where relevant.

  6. Added the column “pass after FDR” to “Table 2: Links to functional enrichment analysis” in the report.html file where relevant.

  7. Matched the PCA sample's colors to the ones in the dendrogarph in the report.html file.

  8. Added the following STAR genomes: Chinese Hamster genome (chok1) and Danio rerio (Zebrafish) version 11 genome (danRer11).

  9. Added bowtie genome - hg38 to the ChIP-Seq and ATAC-seq pipelines.

  10. Changed project name field label to be more informative for the user.

  11. Restricts single cell pipeline to internal users only (BBCU users).

  12. Changed the UTAP emails according to Jaime’s and Marilyn’s requests.