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Feature/dockerize #5

Merged
merged 65 commits into from
Sep 3, 2022
Merged

Feature/dockerize #5

merged 65 commits into from
Sep 3, 2022

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rajewski
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@rajewski rajewski commented Aug 31, 2022 •
edited

This is a major re-write of the repo that

  • Removes the bulky FASTQ files that are saved in this repo and instead downloads the public files from SRA (Closes Pull from SRA #4)
  • Transitions the software decencies from UCR HPCC modules to Docker containers (Closes Docker #1)
  • Updates paths for files to removes absolute paths within the UCR HPCC (Closes Update paths #2)
  • Reorganizes the pipelines inputs, outputs, and references to a more intuitive structure (Closes Organize Directories #3)

@rajewski rajewski added this to the Publication milestone Aug 31, 2022
@rajewski rajewski self-assigned this Aug 31, 2022
@rajewski
update and add R script warning
226181e
@rajewski
Add container for plink #1 and change paths bc of restrictions
aaa91d2
@rajewski
start a graveyard of old scripts that are unnecessary
b4b8341
@rajewski
add faststructure container #1
823b6c7
@rajewski
update JTCoords.csv with better version
d2e607e
@rajewski
graveyard the cophylo plots
03271ec
@rajewski
scratch some old analyses
ae8d3ab
@rajewski
unneeded after #4
1984b5d
@rajewski
redundant files now
3d6cedd
@rajewski
Fix Docker paths
89cc8ba
@rajewski
Reconfigure SplitsTree outs and ins
947c034
@rajewski
combined with other splitstree script
1b8f200
@rajewski
all scripts in one place!
e79b757
@rajewski
Clean up *some* file names
caf20c8
@rajewski
Plotting of MS figures
bbce487
@rajewski
Remove old input data #4
33ca0b9
@rajewski
Theyre all GTR+G+I, so ignore it
ab825c1
@rajewski
weird straggler. I edited this
005089b
@rajewski
unnnedded unless we do bar plots with phylos
d705cae
@rajewski
Duplicated with new dir structure
78a91e0
@rajewski
add outgroups FASTA
50191b0
@rajewski
clean out dup data from Results/PHYLO
0861c96
@rajewski
edit write paths
5e8bc9b
@rajewski
outdated ignores
67e08e0
@rajewski rajewski marked this pull request as ready for review September 3, 2022 00:46
@rajewski
Merge branch 'main' into feature/dockerize
2386f18 
# Conflicts:
#	.gitignore
#	Figure 1.pdf
#	Figure 1.png
#	Figure 2 Alt.pdf
#	Figure 2.pdf
#	Supplemental 2 LFY MDS.pdf
#	Supplemental 2 LFY MDS.png
#	phylo/7h_SplitsNetworks.R
#	phylo/7i_SplitsTreeMDS.R
#	phylo/All Loci Barplot.pdf
#	phylo/LFY/LFY.nex
#	phylo/LFY/LFY.phy
#	phylo/LFY/LFY.phy.reduced
#	phylo/LFY/LFYrenamed.nex
#	phylo/LFY/LFYrenamed.phy
#	phylo/LFY/LFYrenamedJimmy.nex
#	phylo/LFY/LFYrenamedJimmy.phy
#	phylo/SampleMap.pdf
#	phylo/SampleMap.png
#	phylo/WXY/WXY.nex
#	phylo/WXY/WXY.phy
#	phylo/WXY/WXY.phy.reduced
#	phylo/WXY/WXYrenamed.nex
#	phylo/WXY/WXYrenamed.phy
#	phylo/WXY/WXYrenamedJimmy.nex
#	phylo/WXY/WXYrenamedJimmy.phy
#	phylo/concatenated/TESTconcatenated.nex
#	phylo/concatenated/partition.TESTJimmyConcatenated.txt
#	phylo/concatenated/partition.txt
#	phylo/nuclear/Nuclear.cluster1
#	phylo/nuclear/Nuclear.cluster2
#	phylo/nuclear/Nuclear.cluster3
#	phylo/nuclear/Nuclear.eigenval
#	phylo/nuclear/Nuclear.eigenvec
#	phylo/nuclear/Nuclear.irem
#	phylo/nuclear/Nuclear.log
#	phylo/nuclear/Nuclear.mds
#	phylo/nuclear/Nuclear.nosex
#	phylo/nuclear/NuclearH-2C.cluster1
#	phylo/nuclear/NuclearH-2C.cluster2
#	phylo/nuclear/NuclearH-2C.cluster3
#	phylo/nuclear/NuclearH-2C.eigenval
#	phylo/nuclear/NuclearH-2C.eigenvec
#	phylo/nuclear/NuclearH-2C.irem
#	phylo/nuclear/NuclearH-2C.log
#	phylo/nuclear/NuclearH-2C.mds
#	phylo/nuclear/NuclearH-2C.nosex
#	phylo/nuclear/NuclearH8D.cluster1
#	phylo/nuclear/NuclearH8D.cluster2
#	phylo/nuclear/NuclearH8D.cluster3
#	phylo/nuclear/NuclearH8D.eigenval
#	phylo/nuclear/NuclearH8D.eigenvec
#	phylo/nuclear/NuclearH8D.irem
#	phylo/nuclear/NuclearH8D.log
#	phylo/nuclear/NuclearH8D.mds
#	phylo/nuclear/NuclearH8D.nosex
#	phylo/nuclear/NuclearHULL1MDS.pdf
#	phylo/nuclear/NuclearHULL1PC1vPC2.pdf
#	phylo/nuclear/NuclearHULL1PC1vPC3.pdf
#	phylo/nuclear/NuclearHULL1PC2vPC3.pdf
#	phylo/nuclear/NuclearHULL2MDS.pdf
#	phylo/nuclear/NuclearHULL2PC1vPC2.pdf
#	phylo/nuclear/NuclearHULL2PC1vPC3.pdf
#	phylo/nuclear/NuclearHULL2PC2vPC3.pdf
#	phylo/nuclear/NuclearMDS.pdf
#	phylo/nuclear/NuclearMDSLabeled.pdf
#	phylo/nuclear/NuclearMDSSplitsLabeled.pdf
#	phylo/nuclear/NuclearMDSvGeo.pdf
#	phylo/nuclear/NuclearPC1vLat.pdf
#	phylo/nuclear/NuclearPC1vLong.pdf
#	phylo/nuclear/NuclearPC1vPC2.pdf
#	phylo/nuclear/NuclearPC1vPC3.pdf
#	phylo/nuclear/NuclearPC2vLat.pdf
#	phylo/nuclear/NuclearPC2vLong.pdf
#	phylo/nuclear/NuclearPC2vPC3.pdf
#	phylo/nuclear/NuclearPC2vPC4.pdf
#	phylo/nuclear/NuclearPC2vPC5.pdf
#	phylo/nuclear/NuclearPC3vLat.pdf
#	phylo/nuclear/NuclearPC3vLong.pdf
#	phylo/nuclear/NuclearPCvGeo.pdf
#	phylo/nuclear/NuclearSNPSplits.pdf
#	phylo/nuclear/Nuclear_ambig.fasta.nex
#	phylo/nuclear/nuclear_ambig.dist
#	phylo/plastid/Plastid.nex
#	phylo/plastid/Plastid.phy
#	phylo/plastid/Plastid.phy.reduced
#	phylo/plastid/Plastid_NoMissing.nex
#	phylo/plastid/Plastid_NoMissing.phy
#	phylo/plastid/Plastid_NoMissing.phy.reduced
#	phylo/plastid/Plastid_NoMissing_matK.phy
#	phylo/plastid/Plastid_NoMissing_matK.phy.raxml.log
#	phylo/plastid/Plastid_NoMissing_psaA.phy
#	phylo/plastid/Plastid_NoMissing_rpl32.phy
#	phylo/plastid/Plastid_NoMissingrenamed.nex
#	phylo/plastid/Plastid_NoMissingrenamed.phy
#	phylo/plastid/Plastid_NoMissingrenamedJimmy.nex
#	phylo/plastid/Plastid_NoMissingrenamedJimmy.phy
#	phylo/splitstree/LFY.dist.nex
#	phylo/splitstree/LFY.splits.nex
#	phylo/splitstree/Nuclear_ambig.fasta.splits.nex
#	phylo/splitstree/Plastid_NoMissing.dist.nex
#	phylo/splitstree/Plastid_NoMissing.splits.nex
#	phylo/splitstree/TESTconatenated.dist
#	phylo/splitstree/TESTconcatented.splits.nex
#	phylo/splitstree/WXY.dist.nex
#	phylo/splitstree/WXY.splits.nex
#	phylo/splitstree/concatenated.splitstree.nex
@rajewski rajewski merged commit 8419243 into main Sep 3, 2022
@rajewski rajewski mentioned this pull request Sep 3, 2022
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@rajewski rajewski deleted the feature/dockerize branch September 3, 2022 01:11
rajewski added a commit that referenced this pull request Nov 28, 2022
@rajewski
Merge pull request #5 from rajewski/feature/dockerize
def2c83 
Feature/dockerize
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Pull from SRA Organize Directories Update paths Docker
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