>
> Right!  Both working repository are named tgv.  One is at giga/tgv (the 
> real master), and ~/tgv is a copy of the repository on the cluster.  I 
> copied them both to my laptop to work with them.


Local git repository :
gmol16:tgv rjgularte$ git status
On branch master
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

modified:   sequencing/RNAseq/deseq.R


Remote git repository :
gmol16:tgv rjgularte$ git status
On branch master
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

renamed:    sequencing/bam.sort.slq -> sequencing/DNAseq/bam.sort.slq
renamed:    sequencing/bwa.map.q -> sequencing/DNAseq/bwa.map.q
renamed:    sequencing/bwa.map.slq -> sequencing/DNAseq/bwa.map.slq
renamed:    sequencing/fix.headers.txt -> sequencing/DNAseq/fix.headers.txt
renamed:    sequencing/gatk.pp.q -> sequencing/DNAseq/gatk.pp.q
renamed:    sequencing/gatk.pp.slq -> sequencing/DNAseq/gatk.pp.slq
renamed:    sequencing/gatk.ug.q -> sequencing/DNAseq/gatk.ug.q
renamed:    sequencing/order.list -> sequencing/DNAseq/order.list
renamed:    sequencing/ref.index.q -> sequencing/DNAseq/ref.index.q
renamed:    sequencing/vcf.select.sh -> sequencing/DNAseq/vcf.select.sh
renamed:    sequencing/vcf2bed.R -> sequencing/DNAseq/vcf2bed.R
renamed:    sequencing/cuff.analysis.slq -> 
sequencing/RNAseq/cuff.analysis.slq
renamed:    sequencing/deseq.R -> sequencing/RNAseq/deseq.R
renamed:    sequencing/idx_htseq.slq -> sequencing/RNAseq/idx_htseq.slq
renamed:    sequencing/rna.metrics.R -> sequencing/RNAseq/rna.metrics.R
renamed:    sequencing/tophat.map.slq -> sequencing/RNAseq/tophat.map.slq
deleted:    sequencing/mm9.size.txt

Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

deleted:    sequencing/DNAseq/bam.sort.slq
deleted:    sequencing/DNAseq/vcf2bed.R
modified:   sequencing/RNAseq/cuff.analysis.slq
modified:   sequencing/RNAseq/idx_htseq.slq
modified:   sequencing/RNAseq/tophat.map.slq


gmol16:~ rjgularte$ cd giga/tgv/
gmol16:tgv rjgularte$ git merge ~/tgv/
merge: /Users/rjgularte/tgv/ - not something we can merge
gmol16:tgv rjgularte$ git pull ~/tgv/
error: refs/remotes/svn/tags/em_genotypes does not point to a valid object!
>From /Users/rjgularte/tgv
 * branch            HEAD       -> FETCH_HEAD
Already up-to-date.
gmol16:tgv rjgularte$ 


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