smith-chem-wisc Spritz issues

smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data

https://smith-chem-wisc.github.io/Spritz/

MIT License

7 stars 11 forks source link

issues

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update both versions

#242 acesnik closed 4 months ago
0
Update RunnerEngine.cs

#241 acesnik closed 4 months ago
0
Error in rule setup_transfer_mods

#240 trom2 opened 6 months ago
7
Enable running Spritz with singularity

#239 acesnik opened 1 year ago
0
Update SummarizeQuantTab.py

#238 acesnik closed 4 months ago
0
Error in rule make_gene_quant_dataframe_ref

#237 animesh opened 1 year ago
14
Error in rule reorder_genome_fasta

#236 animesh closed 1 year ago
3
Fix version

#235 acesnik closed 1 year ago
0
Fix downloads (versioning fix)

#234 acesnik closed 1 year ago
0
Fix downloads

#233 acesnik closed 1 year ago
0
Error response from daemon: No such container: spritz-615926720

#232 animesh closed 1 year ago
6
Update actions versions

#231 acesnik closed 1 year ago
0
Update some version info

#230 acesnik closed 1 year ago
0
Bump Newtonsoft.Json from 13.0.1 to 13.0.2 in /Spritz/SpritzGUI

#229 dependabot[bot] closed 1 year ago
1
Bump Newtonsoft.Json from 13.0.1 to 13.0.2 in /Spritz/SpritzBackend

#228 dependabot[bot] closed 1 year ago
1
use httpclient

#227 acesnik closed 2 years ago
0
Update uniprot URLs to rest.uniprot from legacy.uniprot

#226 acesnik opened 2 years ago
0
Update mzLib to fix issue downloading psimod

#225 acesnik closed 2 years ago
0
Using Arabidopsis sequences for tests instead of yeast

#224 acesnik opened 2 years ago
1
Fix docker build

#223 acesnik closed 2 years ago
2
Conda/dotnet not properly detecting openssl within minimamba docker container; probable conda issue

#222 acesnik closed 2 years ago
3
FragPipe-ready fasta headers and redundancy reduction

#221 MiguelCos opened 3 years ago
5
Slight discrepancy in number of targets and decoys in `withdecoys.fasta` after mzLib decoy generation

#220 acesnik opened 3 years ago
0
Integration into snakepipes

#219 acesnik closed 3 years ago
1
Simplifying version checks

#218 acesnik closed 2 years ago
1
Add quotes and equals characters to spritzmods commands

#217 acesnik closed 3 years ago
0
Option to generate separate databases for each input

#216 acesnik opened 3 years ago
0
Spritz crashing after command line execution (Ubuntu). Step 10.

#215 MiguelCos closed 3 years ago
14
gatk MarkDuplicates Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded

#214 Stanley80 closed 3 years ago
11
Same issue as #199 with updated mzLib

#213 stsour closed 3 years ago
8
(1) "Error waiting for container: invalid character 'u' looking for beginning of value" (2) "Could not execute because the application was not found or a compatible .NET SDK is not installed."

#212 animesh closed 3 years ago
61
Isoform quantification & restructuring

#211 acesnik closed 3 years ago
0
Still running after five days of computation

#210 Stanley80 closed 3 years ago
4
Use sra-tools 2.10.1 for prefetch/fastq-dump

#209 acesnik closed 3 years ago
0
Add openssh to environment

#208 acesnik closed 3 years ago
0
Improving download speed and setup

#207 acesnik closed 3 years ago
1
Missing input files for rule fastp_fq

#206 puva closed 3 years ago
1
Worflow processing time

#205 mwfoster closed 3 years ago
9
Spritz execution stopped without error messages at step 15/47

#204 llniu closed 3 years ago
10
Error in rule build_transfer_mods

#203 llniu closed 3 years ago
7
Docker vs Nextflow

#202 DrDee79 opened 3 years ago
4
Error in rule reference_protein_xml

#201 animesh closed 3 years ago
5
Update mzLib package

#200 rfellers closed 3 years ago
0
Aborted execution on dotnet TransferUniProtModifications

#199 Stanley80 closed 3 years ago
8
Aborted snakemake execution on command dotnet TransferUniProtModifications/TransferUniProtModifications/bin/Release/netcoreapp3.1/TransferUniProtModifications.dll -x data/uniprot/Homo_sapiens.protein.xml.gz -y /mnt/datasets/spritz/variants/Homo_sapiens.GRCh38.100.protein.xml

#198 Stanley80 closed 3 years ago
0
Improve setup for restricted access servers

#197 acesnik closed 3 years ago
0
Improvements for deploying on HPC clusters; single-end sequencing support

#196 acesnik closed 3 years ago
0
How to run Spritz on HPC environment and how to analyze single End RNAseqs

#195 Jokendo-collab closed 3 years ago
37
Allow RefSeq references to be used

#194 acesnik opened 4 years ago
0
Implement reference-free proteome generation

#193 acesnik opened 4 years ago
0