In [4]: 
ir="/usr/local/bin/irods3.2.icmds.mac.intel/"
In [2]: 
!ils

/bin/sh: ils: command not found
In [8]: 
!{ir}/icd Larvae
In [9]: 
!{ir}/ipwd

/iplant/home/che625/Larvae
In [11]: 
!ils

/iplant/home/che625/Larvae:
  Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa
  C- /iplant/home/che625/Larvae/BSMAP
  C- /iplant/home/che625/Larvae/FastQC_0.10.1__multi-file__analysis1-2014-02-22-11-43-51.881
  C- /iplant/home/che625/Larvae/Nov
  C- /iplant/home/che625/Larvae/Sept
In [12]: 
!ils

/iplant/home/che625/Larvae:
  Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa
  C- /iplant/home/che625/Larvae/BSMAP
  C- /iplant/home/che625/Larvae/FastQC_0.10.1__multi-file__analysis1-2014-02-22-11-43-51.881
  C- /iplant/home/che625/Larvae/Nov
  C- /iplant/home/che625/Larvae/Sept
In [13]: 
!icd /iplant/home/che625/Larvae/BSMAP
In [14]: 
!ils

/iplant/home/che625/Larvae/BSMAP:
  F_R1.fastq
  F_R2.fastq
  M1_R1.fastq
  M1_R2.fastq
  M3_R1.fastq
  M3_R2.fastq
  T1D3_R1.fastq
  T1D3_R2.fastq
  T1D5_R1.fastq
  T1D5_R2.fastq
  T3D3_R1.fastq
  T3D3_R2.fastq
  T3D5_R1.fastq
  T3D5_R2.fastq
  C- /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_F-2014-03-04-17-10-03.726
  C- /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_M1-2014-03-04-17-56-24.707
  C- /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_M3-2014-03-04-17-57-47.804
  C- /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_T1D3-2014-03-04-17-59-25.633
  C- /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_T1D5-2014-03-04-18-00-31.469
  C- /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_T3D3-2014-03-04-18-01-25.753
  C- /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_T3D5-2014-03-04-18-03-28.472
In [21]: 















    Out[21]:






u'/Users/claireellis/Dropbox/Lab (1)/IPython_nbs/Claire'





















In [19]:





!icd /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_F-2014-03-04-17-10-03.726/logs/condor-stdout-F
















In [43]:





!ils 



















/iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_F-2014-03-04-17-10-03.726/logs:
  condor-0-input-0-stderr
  condor-0-input-0-stdout
  condor-0-input-1-stderr
  condor-0-input-1-stdout
  condor-0-input-2-stderr
  condor-0-input-2-stdout
  condor-stderr-0
  condor-stdout-F
  iplant.cmd
  iplant.sh
  output-last-stderr
  output-last-stdout
  script-condor-log
  script-error.log
  script-output.log





















In [25]:





cd



















/Users/claireellis





















In [24]:





!iget /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_F-2014-03-04-17-10-03.726/logs/condor-stdout-F
















In [33]:





!iget /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_M1-2014-03-04-17-56-24.707/logs/condor-stdout-M1 /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output



















ERROR: getUtil: get error for /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output/condor-stdout-M1 status = -312000 OVERWRITE_WITHOUT_FORCE_FLAG
ERROR: getUtil: get error for /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output/condor-stdout-M1 status = -312000 OVERWRITE_WITHOUT_FORCE_FLAG





















In [34]:





!iget /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_M3-2014-03-04-17-57-47.804/logs/condor-stdout-M3 /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output



















ERROR: getUtil: get error for /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output/condor-stdout-M3 status = -312000 OVERWRITE_WITHOUT_FORCE_FLAG





















In [35]:





!iget /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_T1D3-2014-03-04-17-59-25.633/logs/condor-stdout-T1D3 /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output



















ERROR: getUtil: get error for /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output/condor-stdout-T1D3 status = -312000 OVERWRITE_WITHOUT_FORCE_FLAG





















In [36]:





!iget /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_T1D5-2014-03-04-18-00-31.469/logs/condor-stdout-T1D5 /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output



















ERROR: getUtil: get error for /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output/condor-stdout-T1D5 status = -312000 OVERWRITE_WITHOUT_FORCE_FLAG





















In [37]:





!iget /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_T3D3-2014-03-04-18-01-25.753/logs/condor-stdout-T3D3 /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output



















ERROR: getUtil: get error for /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output/condor-stdout-T3D3 status = -312000 OVERWRITE_WITHOUT_FORCE_FLAG





















In [38]:





!iget /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_T3D5-2014-03-04-18-03-28.472/logs/condor-stdout-T3D5 /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output



















ERROR: getUtil: get error for /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output/condor-stdout-T3D5 status = -312000 OVERWRITE_WITHOUT_FORCE_FLAG





















In []: