paths.txt

local:
~/MyDocuments/MobaXterm/scripts
ODER
/home/mobaxterm/MyDocuments/MobaXterm/scripts/scp_loop.sh


#getting data into uppmax: reversing scp download 
scp ./meta.tar.gz rene@milou.uppmax.uu.se:/pica/v14/b2010008_nobackup/database/metacyc/metacyc_20.5


from uppmax:
/proj/b2010008/nobackup/projects/rene_roundup/metag_glyph_workflow/assembly/megahit_coassembly/meta-sensitive/

file transfer:
scp -r rene@milou.uppmax.uu.se:/proj/b2010008/nobackup/projects/rene_roundup/metag_glyph_workflow/taxonomy/metaxa/*.* .
scp -r rene@milou.uppmax.uu.se:/proj/b2010008/nobackup/projects/rene_roundup/metag_glyph_workflow/concoct/meta-sensitive_coassembly/input_kallisto/*.* .
scp rene@milou.uppmax.uu.se:/proj/b2010008/nobackup/projects/rene_roundup/metag_glyph_workflow/annotation/prokka_extended/prokka_output/PROKKA.* .
scp rene@milou.uppmax.uu.se:/proj/b2010008/nobackup/projects/rene_roundup/metag_glyph_workflow/annotation/prokka_extended/prokka_output/megahit_coassembly.0/*.* .
scp rene@milou.uppmax.uu.se:/proj/b2010008/nobackup/projects/rene_roundup/metag_glyph_workflow/concoct/meta-sensitive_coassembly/output_kallisto/cutoff-1000-maxcluster-1000/checkm_output/stats.tsv .
scp rene@milou.uppmax.uu.se:/proj/b2010008/nobackup/projects/rene_roundup/metag_glyph_workflow/annotation/minpath/PROKKA.metacyc20.5.minpath .

#getting concoct output: what contig ids in what bin?
scp rene@milou.uppmax.uu.se:/proj/b2010008/nobackup/projects/rene_roundup/metag_glyph_workflow/concoct/meta-sensitive_coassembly/output_kallisto/cutoff-1000-maxcluster-1000/clustering* .

#getting prokka info: link prokka id to contig id
bash /home/mobaxterm/MyDocuments/MobaXterm/scripts/scp_loop.sh

#getting minpath (not .minpath file)
scp rene@milou.uppmax.uu.se:/proj/b2010008/nobackup/projects/rene_roundup/metag_glyph_workflow/annotation/minpath/MinPath.Metacyc20.5.PROKKA.log .

#getting length of contigs
bash /home/mobaxterm/MyDocuments/MobaXterm/scripts/scp_kallisto_loop.bash