LifeWorks
commented
6 years ago # song.feng @ pn1620056 in ~/working/ivaRnaSeq/PyPiReT-master on git:master x [9:41:21]
$ ./INSTALL.sh
- found conda conda 4.5.0
conda is pointed to right environment
creating piret environment
Solving environment: ...working... done
## Package Plan ##
environment location: /scratch/songfeng/Applications/anaconda3/envs/piret
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use:
# > source activate piret
#
# To deactivate an active environment, use:
# > source deactivate
#
Required version of python (3.6.4) was not found
--------------------------------------------------------------------------
installing python v3.6.4
--------------------------------------------------------------------------------
Solving environment: ...working... done
certifi 2018.1.18: ########## | 100%
openssl 1.0.2o: ########## | 100%
zlib 1.2.11: ########## | 100%
ca-certificates 2018.03.07: ########## | 100%
## Package Plan ##
environment location: /scratch/songfeng/Applications/anaconda3/envs/piret
added / updated specs:
- python=3.6.4
The following packages will be downloaded:
package | build
---------------------------|-----------------
certifi-2018.1.18 | py36_0 144 KB
openssl-1.0.2o | h20670df_0 3.4 MB
zlib-1.2.11 | ha838bed_2 101 KB
ca-certificates-2018.03.07 | 0 124 KB
------------------------------------------------------------
Total: 3.8 MB
The following NEW packages will be INSTALLED:
ca-certificates: 2018.03.07-0
certifi: 2018.1.18-py36_0
libedit: 3.1-heed3624_0
libffi: 3.2.1-hd88cf55_4
libgcc-ng: 7.2.0-hdf63c60_3
libstdcxx-ng: 7.2.0-hdf63c60_3
ncurses: 6.0-h9df7e31_2
openssl: 1.0.2o-h20670df_0
pip: 9.0.3-py36_0
python: 3.6.4-hc3d631a_3
readline: 7.0-ha6073c6_4
setuptools: 39.0.1-py36_0
sqlite: 3.22.0-h1bed415_0
tk: 8.6.7-hc745277_3
wheel: 0.31.0-py36_0
xz: 5.2.3-h55aa19d_2
zlib: 1.2.11-ha838bed_2
Downloading and Extracting Packages
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
------------------------------------------------------------------------------
python v3.6.4 installed
------------------------------------------------------------------------------
- found R version 3.4.3
hisat2 was not found
--------------------------------------------------------------------------
installing hisat2 v2.0.5
--------------------------------------------------------------------------------
Solving environment: ...working... done
## Package Plan ##
environment location: /scratch/songfeng/Applications/anaconda3/envs/piret
added / updated specs:
- hisat2=2.0.5
The following NEW packages will be INSTALLED:
hisat2: 2.0.5-py36pl5.22.0_2 bioconda
libgcc: 7.2.0-h69d50b8_2
perl: 5.22.0.1-0 conda-forge
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
------------------------------------------------------------------------------
hisat2 v2.0.5 installed
------------------------------------------------------------------------------
stringtie was not found
--------------------------------------------------------------------------
installing stringtie v1.3.3
--------------------------------------------------------------------------------
Solving environment: ...working... done
## Package Plan ##
environment location: /scratch/songfeng/Applications/anaconda3/envs/piret
added / updated specs:
- stringtie=1.3.3
The following NEW packages will be INSTALLED:
stringtie: 1.3.3-py36_3 bioconda
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
------------------------------------------------------------------------------
stringtie v1.3.3 installed
------------------------------------------------------------------------------
[1] 1
3.20.1
- found edgeR 3.20.1
[1] 0
NA
- found DESeq2 NA
- found featureCounts
jellyfish was not found
--------------------------------------------------------------------------
installing jellyfish v2.2.6
--------------------------------------------------------------------------------
Solving environment: ...working... done
## Package Plan ##
environment location: /scratch/songfeng/Applications/anaconda3/envs/piret
added / updated specs:
- jellyfish=2.2.6
The following NEW packages will be INSTALLED:
jellyfish: 2.2.6-0 bioconda
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
------------------------------------------------------------------------------
jellyfish v2.2.6 installed
------------------------------------------------------------------------------
- found samtools
bamtools was not found
--------------------------------------------------------------------------
Downloading bamtools v 2.4.0
--------------------------------------------------------------------------------
Solving environment: ...working... done
## Package Plan ##
environment location: /scratch/songfeng/Applications/anaconda3/envs/piret
added / updated specs:
- bamtools=2.4.0
The following NEW packages will be INSTALLED:
bamtools: 2.4.0-3 bioconda
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
--------------------------------------------------------------------------------
bamtools v 2.4.0 installed
--------------------------------------------------------------------------------
gffread is found
FaQCs is not found
------------------------------------------------------------------------------
Installing FaQC
------------------------------------------------------------------------------
Solving environment: ...working... done
certifi 2018.1.18: ########## | 100%
zlib 1.2.11: ########## | 100%
ca-certificates 2018.03.07: ########## | 100%
openssl 1.0.2o: ########## | 100%
## Package Plan ##
environment location: /scratch/songfeng/Applications/anaconda3/envs/piret
added / updated specs:
- zlib=1.2.11
The following packages will be downloaded:
package | build
---------------------------|-----------------
certifi-2018.1.18 | py36_0 144 KB anaconda
zlib-1.2.11 | ha838bed_2 101 KB anaconda
ca-certificates-2018.03.07 | 0 124 KB anaconda
openssl-1.0.2o | h20670df_0 3.4 MB anaconda
------------------------------------------------------------
Total: 3.8 MB
The following packages will be UPDATED:
ca-certificates: 2018.03.07-0 --> 2018.03.07-0 anaconda
certifi: 2018.1.18-py36_0 --> 2018.1.18-py36_0 anaconda
openssl: 1.0.2o-h20670df_0 --> 1.0.2o-h20670df_0 anaconda
zlib: 1.2.11-ha838bed_2 --> 1.2.11-ha838bed_2 anaconda
Downloading and Extracting Packages
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
FaQCs/FaQCs.cpp
FaQCs/fastq.cpp
FaQCs/file_util.cpp
FaQCs/options.cpp
FaQCs/plot.cpp
FaQCs/seq_overlap.cpp
FaQCs/trim.cpp
FaQCs/VTrim.cpp
FaQCs/FaQCs.h
FaQCs/fastq.h
FaQCs/file_util.h
FaQCs/matrix.h
FaQCs/seq_overlap.h
FaQCs/shave.h
FaQCs/ChangeLog.txt
FaQCs/Makefile
g++ -O3 -Wall -fopenmp -std=c++0x -msse2 -DATA16 -I. -c fastq.cpp
In file included from fastq.cpp:2:0:
fastq.h:6:10: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^~~~~~~~
compilation terminated.
Makefile:18: recipe for target 'fastq.o' failed
make: *** [fastq.o] Error 1
FaQCs/FaQCs.cpp FaQCs/fastq.cpp FaQCs/file_util.cpp FaQCs/options.cpp FaQCs/plot.cpp FaQCs/seq_overlap.cpp FaQCs/trim.cpp FaQCs/VTrim.cpp FaQCs/FaQCs.h FaQCs/fastq.h FaQCs/file_util.h FaQCs/matrix.h FaQCs/seq_overlap.h FaQCs/shave.h FaQCs/ChangeLog.txt FaQCs/Makefile g++ -O3 -Wall -fopenmp -std=c++0x -msse2 -DATA16 -I. -c fastq.cpp In file included from fastq.cpp:2:0: fastq.h:6:10: fatal error: zlib.h: No such file or directory
include
compilation terminated. Makefile:18: recipe for target 'fastq.o' failed make: *** [fastq.o] Error 1