XPRESSpipe-v0.6.4

What's Changed

• Update test cases
• Add frozen requirements yml to aid in installation
• Add more explicit R installs
• Fixed compiled plotting - more graceful errors
• Fixed GTF partitioning for edits for more graceful checks

Full Changelog: v0.6.3...XPRESSpipe-v0.6.4

XPRESSpipe-v0.6.3

Major

• New installation method: Instead of installing the software with the pip install . method, a new install script is provided that handles installation of some dependencies better. The new method now only requires the user to run bash install.sh. See the Installation page for an updated walkthrough on this update.

Minor

• Updated docs and examples
• Removed unused variable in args_dict

XPRESSpipe-v0.6.2

• Added --suppress_version_check flag to enable use of XPRESSpipe without internet access
• Added --smoothen flag to any module that uses the geneCoverage sub-module. By default, a sliding window will not be used to smoothen the geneCoverage plots. If provided, a rolling window set at 20 will be used to smoothen the plots.

conda-freeze-v0.6.2.txt
r-freeze-v0.6.2.txt

XPRESSpipe-v0.6.1

• Added flag during curation steps to allow of UCSC/refseq GTFs during GTF modification steps (truncation, etc.)
  Usage: Provide the --ucsc_format flag to the curateReference or modifyGTF sub-modules. These modifications in format only apply to XPRESSpipe GTF truncation features. Any formatting errors with the GTF file that pertain to alignment, counting, etc. dependencies will need to be addressed by the user.
• Fixed error in XPRESSpipe interface with XPRESSplot’s convert_names function where XPRESSpipe did not read in first column of table as index

freeze_v0.6.1.txt

XPRESSpipe-v0.6.0

• Minor modification to instructions on how to install XPRESSpipe and use its conda environment on a supercomputing node.
• Removed version specifications for conda environment setup to ease install (fixes issues in a better way than the solution from v0.5.0)
• Moved required riboWaltz functions to XPRESSpipe as installation has been recurrently problematic

Working conda environment: freeze_v0.6.0.txt

XPRESSpipe-v0.5.0

• Fixed issue where genome size calculation would round up and miscalculate genome_size parameter for STAR.
• Added fastp_lite for removal of 3' internal UMIs (generally takes ~1 min per RNA-seq sample with about 30 million reads)
• For example: 5'-read-spacer-UMI-adapter-3'
  • Integrating this addition into options and trimming
• Updated MANIFEST file to reliably copy R and Julia scripts to executing folder for XPRESSpipe
• Updated command builder (xpresspipe build) to include recent additions
• Updated requirements to prevent issue where solved environment required to install R 3.5.1 or greater would create an error where samtools markdup would freeze
• Frequently, R 3.5.1 or greater would create library linking error to stringi, causing GenomicFeatures to not function. Added to RbuildIndex.r to reinstall stringi, which appears to clear up the issue.

Most recent working conda environment dependencies: freeze_v0.5.0.txt

XPRESSpipe-v0.4.4

Fixed critical error with string catenation during fastp call with UMIs (see #38).

XPRESSpipe-v0.4.3

• Fixed issue with metagene where parallelization overloaded memory and resulted in OOM errors. Fixed by making memory thresholding slightly more strict. See #37

XPRESSpipe-v0.4.2

• Slight modification to convert_names module

XPRESSpipe-v0.4.1

Minor release

• Introduced some restrictions to dependency versions. Some newer versions of dependencies were acting problematic. Will try to figure out how to allow for current versions of these dependencies to be used
• Fixed plotting issue with periodicity plots